Genetic analysis systems and methods

ABSTRACT

Improved systems and methods for performing genetic analyses. Full genomic DNA scans are performed on the genetic DNA from a plurality of individuals to identify genetic variants. For those variants, but not based on a full genetic DNA scan, the variants alone are scanned in additional individuals to identify blocks of the variants that tend to be inherited together.

BACKGROUND OF THE INVENTION

[0001] The DNA that makes up human chromosomes provides the instructionsthat direct the production of all proteins in the body. These proteinscarry out the vital functions of life. Variations in DNA often producevariations in the proteins, thus affecting the function of cells.Although environment often plays a significant role, variations ormutations in DNA are directly related to almost all human diseases,including infectious disease, cancer, inherited disorders, andautoimmune disorders. Moreover, knowledge of human genetics has led tothe realization that many diseases result from either complexinteractions of several genes or from any number of mutations within onegene. For example, Type I and II diabetes have been linked to multiplegenes, each with its own pattern of mutations. In contrast, cysticfibrosis can be caused by any one of over 300 different mutations in asingle gene.

[0002] Additionally, knowledge of human genetics has led to a limitedunderstanding of differences between individuals when it comes to drugresponse—the field of pharmacogenetics. Since the first correlation overhalf a century ago of adverse drug responses with amino acid variationsin two drug-metabolizing enzymes, plasma cholinesterase andglucose-6-phosphate dehydrogenase, careful genetic analyses have linkedsequence polymorphisms in over 35 drug metabolism enzymes, 25 drugtargets and 5 drug transporters with compromised levels of drug efficacyor safety. In the clinic, such information is being used to prevent drugtoxicities; for example, patients are often screened for geneticdifferences in the thiopurine methyltransferase gene that causedecreased metabolism of 6-mercaptopurine or azathiopurine. Yet only asmall percentage of observed drug toxicities have been explainedadequately by the set of pharmacogenetic markers validated to date. Inaddition, insufficient therapeutic efficacy or unanticipated sideeffects in “outlier” individuals when administered drugs previouslydemonstrated to be both safe and efficacious in clinical trials is atremendous problem for health care practitioners and presents asignificant dilemma to the pharmaceutical industry.

[0003] Disease-related and pharmacogenetic gene validation relies onelements of population and quantitative genetics and robust statisticalmetrics; however, the first step normally relies upon identification ofa candidate target gene. To date, various biotechnological methods havebeen employed to identify candidate genes. For example, differentialgene expression has been employed, essentially looking for differencesin gene expression between affected and unaffected individuals orbetween treated and untreated individuals. In addition, protein-proteininteraction maps to identify drug receptors and their immediateeffectors have been used. Another approach involves mining humansequence databases for sequences similar to accepted disease-related orpharmacokinetic or pharmacodynamic regulators.

[0004] Because any two humans are 99.9% similar in their genetic makeup,most of the sequence of the DNA of their genomes is identical. However,there are variations in DNA sequence between individuals. For example,there are deletions of many-base stretches of DNA, insertion ofstretches of DNA, variations in the number of repetitive DNA elements innoncoding regions, and changes in single nitrogenous base positions inthe genome called “single nucleotide polymorphisms” or “SNPs”. It isestimated that there are 3 to 4 million common SNPs that occur in atleast 10 percent of people. These common SNPs do not occur independentlybut are passed from generation to generation in variable-length blocksof multiple SNPs, forming patterns across the genome. Such blocks ofSNPs are called SNP haplotype blocks herein.

[0005] The candidate gene identification strategy most relevant to SNPsis whole-genome association on various populations of individuals-thatis, scanning the entire genomes of populations of individuals tocorrelate SNPs to disease or drug response. Such whole-genome analyseswould provide a fine degree of genetic mapping and pinpoint specificregions of linkage. Methods have been proposed and are used inconnection with whole genome analysis. For example, the methodsdescribed in U.S. Ser. No. 60/327,006, filed Oct. 5, 2001, “IdentifyingHuman SNP Haplotypes, Informative SNPs and Uses Thereof,” assigned tothe assignee of the present invention (Attorney docket no.054801-5001-P2; 1005-P3, incorporated herein by reference for allpurposes) have been proposed for use in such applications. U.S. Ser. No.unassigned, filed Sep. 18, 2001, “Human Genomic Polymorphisms”, assignedto the assignee of the present invention (Attorney Docket no.10108319/1013P-1) incorporated herein by reference for all purposes,provides the identity of SNPs and SNP haplotype blocks across onerepresentative chromosome, ie. Chromosome 21.

[0006] While meeting with success, it is desirable to increase the speedand efficiency at which such analyses can be performed, as well as todecrease the cost of performing such analyses.

SUMMARY OF THE INVENTION

[0007] Improved methods, devices, and systems for performing geneticanalysis are provided. According to one embodiment of the invention amethod is provided in which genetic DNA or derivatives therefrom isscanned from a plurality of individuals. The scanning uses, for example,a gel based sequencer or high density array to identify geneticpolymorphisms in a plurality of individuals. For the polymorphisms thatoccur in a plurality of individuals, but not all of the scanned bases,genetic DNA or derivatives therefrom from additional individuals isevaluated to identify which of the variants occur in the additionalindividuals. Based the results of scanning the additional individuals,the method provides for the identification of blocks of thepolymorphisms that tend to be inherited together. The blocks ofpolymorphisms can then be used in a wide variety of applications such asdrug target identification, identification of diagnostics, clinicaltrial evaluation, pharmacogenomics, and other applications.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0008] Throughout the disclosure various patents, patent applicationsand publications are referenced. Unless otherwise indicated, each isincorporated by reference in its entirety for all purposes.

[0009] U.S. Ser. No. 60/327,006, filed Oct. 5, 2001, “Identifying HumanSNP Haplotypes, Informative SNPs and Use Thereof,” assigned to theassignee of the present invention (Attorney docket no. 054801-5001-P2)incorporated herein by reference for all purposes, describes methods foridentifying single nucleotide polymorphisms, assigning suchpolymorphisms to groups, and using such groups in the drug discoveryprocess. FIG. 1 provides an overall diagram illustrating such processes.In FIG. 1, variant locations in a genome, such as the human genome, areidentified in step 110. The processes used in step 110 can include, forexample, scanning genomic regions for variants using DNA/RNA arrays suchas those available from Affymetrix, Inc. (such as discussed in generalin U.S. Pat. No. 5,861,242, incorporated herein by reference for allpurposes), the use of conventional gel sequencing techniques such asthose based on gel sequencers available from Applied Biosystems, Inc.,capillary sequencing techniques, or other techniques. Preferably, onlycommon SNPs, such as those that occur in more than 10% of the populationin question, are used in the analysis since, for example, these SNPswill represent evolutionarily older variants and, therefore, tend tocorrelate with more common diseases/states in a larger fraction of thepopulation.

[0010] In preferred embodiments, the genomic DNA (or a derivativetherefrom, such as PCR DNAs or RNA amplicons or the like) is scanned forvariants using a high density DNA array. Using one technology, an arrayof probes is formed on a high density array. The array of probesincludes a) probes that are complementary to portions of a baselinesequence of the genetic DNA (such as that obtained from a first passsequencing effort) and b) one or more probes that are complementary tovariants of the baseline sequence of the genetic DNA. The genetic DNA,or a derivative thereof, is then labeled and hybridized to the array andscanned. Based on the locations where hybridization is detected one candetect whether the bases in the genetic DNA are “wild type” or variant.In the cases where the particular base is the same as the referencesequence, the labeled material will hybridize more strongly to the wildtype probe. In those cases where the DNA sequence varies from thereference sequence, the labeled material will hybridize more strongly toone of the variant probes. Based on this information, one can call aparticular base as being the same or variant from the referencesequence.

[0011] In preferred embodiments, more than 10,000 bases are scanned forvariants. In more preferred embodiments, more than 1×10⁶ bases arescanned for variants, more preferably more than 2×10⁶ bases, morepreferably 1×10⁷, and more preferably more than 1×10⁸, and morepreferably more than 1×10⁹ bases are scanned for variants. In preferredembodiments at least introns are scanned for variants, and in morepreferred embodiments both introns and exons are scanned for variants.In preferred embodiments the scanned nucleic acids are genomic DNA. Inmost preferred embodiments, such DNA is from a mammalian organism suchas a human. In preferred embodiments, more than 10% of the genomic DNAfrom the organism is scanned, in more preferred embodiments more than25% of the genomic DNA from the organism is scanned, in more preferredembodiments, more than 50% of the genomic DNA from the organism isscanned, and in most preferred embodiments, more than 75% of the genomicDNA is scanned.

[0012] In step 120 the variants are assigned to groups. Such groups ofvariants are blocks of variants (in most cases, single nucleotidepolymorphisms or “SNPs”) that tend to be inherited together. Such“blocks” or “SNP variant haplotype blocks” have likely arisen from anevolutionary point of view because the edges of blocks will tend to bethe boundaries of ancient recombination events in the species. In step130, representative variants from each block are used in an associationstudy to identify associations of such blocks to a phenotype. Suchassociation studies may be run using a variety of technologies such asa) Affymetrix genotyping arrays, b) “Invader” assays available fromThird Wave, such as described in Agarwal, P. et al. “Comparison studyfor identifying promoter allelic polymorphism in interleukin 10 andtumor necrosis factor alpha genes”, Diagn Mol Pathol 9, 158-64(2000);Cooksey, R. C., Holloway, B. P., Oldenburg, M. C., Listenbee, S. &Miller, C. W. “Evaluation of the Invader assay, a linear signalamplification method, for identification of mutations associated withresistance to rifampin and isoniazid in Mycobacterium tuberculosis”Antimicrob Agents Chemother 44, 1296-301 (2000); and Mein, C. A. et al.“Evaluation of single nucleotide polymorphism typing with Invader on PCRamplicons and its automation” Genome Res 10, 330-43 (2000), allincorporated herein by reference, or c) “Taqman” assays, such asdescribed in Arnold, B. A., Hepler, R. W., and Keller, P. M. “One-StepFluorescent Probe Product-Enhanced Reverse Transcriptase Assay”BioTechniques 25(1):98-106, 1998; Becker K., D. Pan and C. B. Whitley.1999. Real-time quantitative polymerase chain reaction to assess genetransfer. Hum. Gene Ther. 10:2559-2566, 1999; Berg, T., Miller, A. R.,Platz, K. P., Hohne, M., Bechstein, W. O., Hopf, U., Wiedenmann, B.,Neuhaus, P., and Schreier, E. “Dynamics of GB virus C viremia earlyafter orthotopic liver transplantation indicates extrahepatic tissues asthe predominant site of GB virus C replication” Hepatology29(1):245-249, 1999; or a variety of other technologies. When arraybased technologies are used, as an example, one makes arrays similar tothose described above, except that only the variant positions are“tiled” onto the array.

[0013] Once it has been determined which regions of the genome areassociated with, for example, a disease state, drug screening assays arerun to identify one or more molecules that mediate the relevant portionsof the genome in step 140 to identify therapeutics 150. In addition, theassociations themselves may be used directly in genetic diagnosticassays, immunoassays or other diagnostic tests in step 160. Inalternative embodiments the variant regions are used in studies toevaluate drug response such as in pharmacogenomic studies. The resultsare then used to stratify patents according to drug response. Thestratification may, in some embodiments, be used to stratify individualsthat may exhibit a toxic response from those that will not. In othercases, the stratification may separate those that will be non-respondersfrom those who will be responders.

[0014]FIG. 2 provides one illustration of showing how variants, usuallySNPs, occur in groups or blocks in a genome. Such SNP haplotype blocksare chromosomal regions that tend to be inherited as a unit, with arelatively small number of common forms. Each line in FIG. 2 representsportions of the haploid genome sequence of different individuals. Asshown therein, individual W has an “A” at position 241, a “G” atposition 242, and an “A” at position 243. Individual X has the samebases at positions 241, 242, and 243. Conversely, individual Y has a Tat positions 241 and 243, but an A at position 242. Individual Z has thesame bases as individual Y at positions 241, 242, and 243. The variantswill most commonly be biallelic, ie. occur in only one of 2 forms, notall four possibilities. Variants in block 261 will tend to occurtogether. Similarly, the variants in blocks 262 and 263 will tend tooccur together. Of course, only a few bases in a genome are shown inFIG. 2. In fact, most bases will be like those at position 245 and 248,and will not vary from individual to individual.

[0015] This tendency of SNPs to occur together in SNP haplotype blocksallows for a single or a few SNPs in a block to be used in anassociation study, rather than all of the SNPs in that block. Forexample, by evaluating only the SNP at position 241, the SNPs atpositions 242 and 243 can be predicted without performing an assay toidentify SNPs 242 and 243. If position 241 contains an A, position 242will contain a G and position 243 will contain an A. Conversely, ifposition 241 contains a T, positions 242 and 243 respectively willcontain an A and a T respectively. Similarly, a SNP in block 262 can beused to predict the other SNPs in block 262. For example, if SNP 244 isa T, it will be known that position 246 is a C, and position 247 is a G.Conversely, if position 244 is a C, position 246 is an A, and position247 is a C.

[0016] According to the invention herein, all or substantially all ofthe bases in a genomic region are scanned for common SNPs in a first,limited, sample set. Then, using substantially only those SNPsidentified in the first scanning step, additional individuals aregenotyped at those SNP locations that are identified from a full scan ofthe genomic region of interest. The first sample set is sufficientlylarge that the full scan of genomic DNA identifies a sufficient numberof SNPs with a sufficiently high level of confidence, but is not largeenough to necessarily identify all of the block boundaries to anecessary level of confidence for the particular experiment. The secondsample set is of a sufficient size that it will allow definition ofblock boundaries with a sufficient level of confidence for theexperiment.

[0017]FIG. 3 illustrates the process in greater detail. As shown, atstep 310 a subset of “n” genomic DNAs are scanned across all or aportion such genomes at every base location for common SNPs or variants.Thereafter, using genotyping technologies such as those described above,only those variant locations identified in step 310 are used to genotypean additional “m” individuals. Using the genotypes accumulated fromsteps 310 and 320, variant blocks are assigned. Using the inventionherein, the cost and burden of performing genetic analysis, especiallywhole genome analysis, is significantly reduced since, for a fraction ofthe population analyzed, only a fraction of the bases of the genomic DNAof interest needs to be evaluated in assigning variants to respectiveblocks.

[0018] In preferred embodiments, copies of more than 10 differentmonoploid genomic DNAs are scanned for variants at step 310 to be usedin the further genotyping analysis (i.e. “n” is 10 or more). In morepreferred embodiments more than 15 different copies of the genomic DNAare scanned for variants to be used in the further genotyping analysis(i.e. “n” is 15 or more). In more preferred embodiments more than 18copies of the genomic DNA are scanned for variants to be used in thefurther genotyping analysis (i.e. “n” is 18 or more). In more preferredembodiments more than 20 genomic DNAs are scanned for variants to beused in the further genotyping analysis (i.e. “n” is 20 or more). Inmore preferred embodiments more than 25 copies of the genomic DNA arescanned for variants to be used in the further genotyping analysis (i.e.“n” is 25 or more).

[0019] In preferred embodiments, the full scanning of genomic DNA isfollowed up by genotyping at step 320 of additional samples to evaluaterepresentative SNPs discovered in the full scans. In preferredembodiments, the genotyping step 320 analyzes more than 10 differentmonoploid genomic DNAs (ie. “m” is 10 or more). In more preferredembodiments, the genotyping step 320 analyzes more than 15 differentgenomic DNAs. In more preferred embodiments, the genotyping step 320analyzes more than 20 different genomic DNAs. In more preferredembodiments, the genotyping step 320 analyzes more than 25 differentgenomic DNAs. In more preferred embodiments, the genotyping step 320analyzes more than 30 different genomic DNAs.

[0020]FIG. 4 illustrates the outcome of the process of FIG. 3 in ahypothetical situation. The top portion of FIG. 4 illustrates thesequence of a hypothetical stretch of DNA, with the variant positionsindicated and variant block boundaries drawn. Of course, the top portionof FIG. 4 illustrates the stretch of genomic DNA with mutations markedand the block boundaries drawn, although this information would not beknown ab initio. Sequencing results 410 show the results of sequencinghaploid DNA of 3 individuals. As shown, in general it is possible tohave identified a large fraction of the common SNPs after a relativelysmall number of individuals have been sequenced. In the case in FIG. 4,the SNPs at each location shown in the top portion of FIG. 4 have beenidentified, as indicated by check marks. However, if further individualsare not evaluated, the block boundaries would not be correctlyidentified at this stage. For example, while one could at this stagedraw block boundaries between blocks 420 and 430 (note that the firstC→G variant predicts the first G→A variant, and the first C→T variantpredicts the second C→T variant), it is not possible to distinguishbetween the blocks 430 and 440 at this stage. At this stage it appearsthat the first C→T variant would predict the first and second T→Avariants. Accordingly, a more statistically significant sample set isrequired to draw the block boundaries. However, since relevant SNPs havebeen identified, it is now possible to genotype only the variantpositions to complete the process of identifying block boundarieswithout sequencing the entire stretch of genomic DNA.

[0021] The results of performing a genotyping process on only the SNPsin another hypothetical genomic sample are shown in FIG. 4 at 420. Asshown, by performing this additional genotyping step, it is now possibleto see that blocks 430 and 440 are distinguishable. Specifically, it isnow possible to see that the first C→T variant does not track with thefirst and second T→A variants, but instead, the first C→T variant can beused to predict only the second C→T variant and the first T→A variantcan be used only to predict the second T→A variant.

[0022] Without wishing to be bound by any particular theory ofoperation, it is believed that the basis on which the assays may besuccessfully utilized in this manner is found in the fact that a fewindividuals may be used to find the most common SNPs. The most commonhaplotypes account for most individuals, but less common haplotypescould be mis-ordered in terms of frequency of occurrence if a largersample set is not used.

EXAMPLE(s)

[0023] Using Affymetrix whole wafers, a region of genomic DNA fromchromosome 21 was scanned for polymorphic regions, generally using themethods of U.S. Ser. No. 60/327,006, filed Oct. 5, 2001, “IdentifyingHuman SNP Haplotypes, Informative SNPs and Use Thereof,” assigned to theassignee of the present invention (Attorney docket no. 054801-5001-P2;1005-P3, incorporated herein by reference for all purposes). 19additional copies of chromosome 21 were then evaluated using the sametechniques. “Common” SNPs were evaluated, meaning those that occur withan allele frequency of more than 10% in this particular example. Toevaluate whether one may use 19 scans for SNP detection, rather than 38,it was determined how many SNPs would produce an allele frequencyof >10% across all 38 scans, but are not considered common polymorphismin a set of just 19 scans. To have an allele frequency of >10% out of38, a SNP would need to have a frequency of >20% in 19 scans, if it isnot polymorphic at all in the other 19 scans. In the analysis performed,89% of common SNPs were identified by evaluating just 19 scans. SNPsidentified in the above analysis are shown in Tables 1, 2, and 3. Table1 shows the SNPs that would have been found in both of the first andlast 19 scans of a 38 scan set. Table 2 shows the SNPs that would havebeen identified by evaluating the first 19 of the 38 scans of chromosome21, but would not have been identified by evaluating only the second 19scans. Table 3 shows the SNPs that would have been identified byevaluating the last 19 of 38 scans of chromosome 21, but would not havebeen identified by evaluating only the first 19 scans. There are 3170SNPs identified in both the first and last 19 scans. There are 361 SNPsfound in only the first 19 scans, and 516 in only the second 19 scans.Therefore, there are ((0.5)* (361+516))/(3170+361+516) or 11% of theSNPs, on average, that would not be found in only half of the number ofscans in chromosome 21. TABLE 1 POSITION REFERENCE_BASE ALTERNATE_BASE  1: 13780263 a g   2: 13780367 c t   3: 13780384 g a   4: 13781532 a g  5: 13782288 t c   6: 13782368 t c   7: 13787259 t c   8: 13788521 t c  9: 13790624 g a  10: 13793189 c a  11: 13793483 t c  12: 13793851 t c 13: 13793902 c a  14: 13793923 a g  15: 13794104 g c  16: 13794163 t c 17: 13794309 a c  18: 13794556 g t  19: 13795184 c g  20: 13795310 a g 21: 13796245 c t  22: 13797171 a g  23: 13798473 a t  24: 13798594 c t 25: 13799031 a t  26: 13799116 a g  27: 13799679 a g  28: 13799935 g a 29: 13800043 g t  30: 13800201 a g  31: 13800956 t c  32: 13801272 c t 33: 13801560 c g  34: 13804651 c t  35: 13805013 g a  36: 13805107 c t 37: 13805416 c t  38: 13805691 g a  39: 13806436 t c  40: 13808142 g c 41: 13808771 t c  42: 13808776 c t  43: 13808906 g a  44: 13809243 t g 45: 13809448 g a  46: 13809729 c g  47: 13809964 c t  48: 13810532 a g 49: 13811589 g c  50: 13812436 g c  51: 13829193 a g  52: 13837787 c a 53: 13843201 g t  54: 13843560 c t  55: 13844156 a g  56: 13845008 g c 57: 13850206 g t  58: 13850467 a t  59: 13850793 g c  60: 13851331 g a 61: 13851465 t c  62: 13851482 g a  63: 13851839 a t  64: 13853325 t g 65: 13854406 t c  66: 13855468 g a  67: 13857664 g a  68: 13859884 g c 69: 13861361 t c  70: 13862014 g c  71: 13862811 a c  72: 13864035 c t 73: 13864454 g t  74: 13865342 c t  75: 13869013 c t  76: 13870959 a t 77: 13870981 a g  78: 13872382 a g  79: 13872723 a t  80: 13874188 a g 81: 13875913 a g  82: 13876910 a g  83: 13877368 t a  84: 13877712 g a 85: 13877854 t c  86: 13880011 c t  87: 13880770 g a  88: 13883076 c t 89: 13883341 t g  90: 13883511 a g  91: 13883719 c t  92: 13884172 g a 93: 13884439 a g  94: 13884476 c t  95: 13885037 c t  96: 13888038 a t 97: 13888604 g t  98: 13889436 t c  99: 13890344 g a  100: 13890511 g a 101: 13891102 a t  102: 13891894 a g  103: 13891974 g a  104: 13892019t c  105: 13892406 a t  106: 13892423 a g  107: 13892460 c a  108:13892533 c t  109: 13892640 t c  110: 13894072 g a  111: 13894132 c a 112: 13894680 a g  113: 13895433 g a  114: 13901024 t g  115: 13902432t g  116: 13903639 c g  117: 13904140 g a  118: 13905359 c t  119:13906874 a g  120: 13908702 t g  121: 13923816 a g  122: 13924410 g c 123: 13928582 g a  124: 13929428 g a  125: 13932906 g a  126: 13934231a c  127: 13934282 t c  128: 13934468 t c  129: 13934480 a c  130:13934691 t c  131: 13936168 t c  132: 13939719 g t  133: 13945313 g c 134: 13945619 t c  135: 13946328 t c  136: 13948558 t c  137: 13957861t c  138: 13957897 a g  139: 13961188 t c  140: 13961398 a c  141:13963166 t a  142: 13963226 a g  143: 13964526 t g  144: 13965988 a c 145: 13967031 a g  146: 13967361 a c  147: 13968052 c g  148: 13968186a g  149: 13968704 t g  150: 13968772 g a  151: 13969447 c g  152:13969802 t g  153: 13969816 t a  154: 13969885 g a  155: 13969965 a c 156: 13970342 t c  157: 13971387 t a  158: 13971823 c t  159: 13983563g a  160: 13985003 a g  161: 13985280 t g  162: 13985454 g a  163:13985887 a c  164: 13986661 t c  165: 13987607 a g  166: 13988282 c t 167: 13989518 t c  168: 13989987 c t  169: 13991021 c a  170: 13991140a g  171: 13991288 a g  172: 13992670 t c  173: 13992705 c t  174:13994022 c t  175: 13996917 t c  176: 13997836 g c  177: 13998686 t a 178: 13998835 g a  179: 13999356 t a  180: 14018678 a c  181: 14018887t g  182: 14019896 c t  183: 14024121 g a  184: 14024187 a t  185:14024852 c g  186: 14024923 a t  187: 14028090 g a  188: 14028399 c t 189: 14028430 g a  190: 14029873 g a  191: 14031210 g t  192: 14032972c t  193: 14033384 t a  194: 14034385 g a  195: 14038441 g c  196:14038480 a g  197: 14038639 t c  198: 14040439 c g  199: 14040876 g a 200: 14041428 c t  201: 14041932 a g  202: 14043266 c t  203: 14044634a g  204: 14045104 a g  205: 14045200 a g  206: 14048027 c t  207:14048350 c t  208: 14049343 g a  209: 14050138 g a  210: 14050258 g a 211: 14051897 c t  212: 14052199 c t  213: 14053863 a g  214: 14055606g t  215: 14055656 a g  216: 14056221 a g  217: 14056375 g a  218:14056470 c t  219: 14057430 t c  220: 14059144 c t  221: 14060584 t c 222: 14060804 g c  223: 14061225 c t  224: 14064737 t a  225: 14067569a g  226: 14068069 a t  227: 14068127 t g  228: 14069638 t c  229:14070973 t c  230: 14072067 a t  231: 14078398 g a  232: 14079489 c t 233: 14080941 a c  234: 14082287 g a  235: 14082513 a g  236: 14083192t g  237: 14083520 t c  238: 14087424 t a  239: 14087441 g a  240:14088548 g a  241: 14091100 c g  242: 14092256 c t  243: 14093151 c g 244: 14094373 t c  245: 14096443 g t  246: 14097696 g a  247: 14098656a c  248: 14101014 g t  249: 14102964 g a  250: 14105489 a g  251:14105717 c t  252: 14106349 t g  253: 14106571 t c  254: 14106827 g a 255: 14106974 t c  256: 14108664 c t  257: 14108889 c g  258: 14109194c t  259: 14109540 a g  260: 14109875 a g  261: 14109953 t c  262:14109982 t c  263: 14110042 c t  264: 14110270 c t  265: 14110383 t c 266: 14110462 c t  267: 14110527 c a  268: 14112293 t g  269: 14112571c t  270: 14114928 c t  271: 14115291 a g  272: 14116560 g a  273:14117021 a g  274: 14117699 g c  275: 14117814 a g  276: 14118003 a g 277: 14118769 t c  278: 14121320 a g  279: 14121579 t c  280: 14121866t g  281: 14122772 t c  282: 14122865 a g  283: 14124291 a g  284:14124472 c t  285: 14124593 g c  286: 14125680 t c  287: 14129043 a g 288: 14129176 c g  289: 14130516 g a  290: 14130838 t c  291: 14131390a c  292: 14131972 c t  293: 14132126 t c  294: 14132401 a g  295:14134814 t c  296: 14135469 a g  297: 14136092 a c  298: 14136237 a g 299: 14136296 c t  300: 14136795 t c  301: 14136889 a g  302: 14137167c t  303: 14137397 a g  304: 14137990 g a  305: 14138306 g a  306:14140410 t c  307: 14140637 g a  308: 14140847 a g  309: 14140940 c t 310: 14142190 c t  311: 14143299 g a  312: 14148398 t c  313: 14148765a t  314: 14149402 g c  315: 14150692 t c  316: 14150844 c t  317:14151614 t c  318: 14151757 t a  319: 14152283 c a  320: 14152410 c a 321: 14152443 a g  322: 14152519 a g  323: 14153887 t g  324: 14154251g t  325: 14154271 a g  326: 14154689 a g  327: 14154783 t c  328:14154976 a t  329: 14155259 c t  330: 14155374 c t  331: 14155524 c g 332: 14155638 g a  333: 14156729 c t  334: 14157020 g a  335: 14157103a g  336: 14158286 t c  337: 14162213 g c  338: 14164467 c t  339:14166866 a c  340: 14167915 g a  341: 14170156 g a  342: 14173042 a g 343: 14173477 c t  344: 14174757 t c  345: 14176517 c t  346: 14176757t c  347: 14176972 g a  348: 14177117 g a  349: 14181577 g a  350:14182229 c t  351: 14182354 g t  352: 14184334 g a  353: 14184808 g a 354: 14185989 t c  355: 14186027 a g  356: 14188115 a g  357: 14190855t g  358: 14192479 a g  359: 14193521 t c  360: 14194389 g a  361:14198173 c g  362: 14201219 a g  363: 14202630 t c  364: 14203012 t c 365: 14203271 a g  366: 14203553 c t  367: 14203777 a c  368: 14203951g a  369: 14204809 g a  370: 14207361 c t  371: 14207605 g a  372:14207771 c t  373: 14207834 a g  374: 14208286 a t  375: 14208359 t c 376: 14208434 c t  377: 14208530 t c  378: 14208685 c t  379: 14208750t a  380: 14208793 c t  381: 14209006 c t  382: 14209020 a t  383:14209282 c t  384: 14209654 t c  385: 14209703 t c  386: 14210273 a c 387: 14211548 c t  388: 14212470 g a  389: 14214548 g c  390: 14214851t c  391: 14217859 g a  392: 14218529 a g  393: 14218614 a t  394:14221089 a g  395: 14221164 a g  396: 14221292 g a  397: 14221430 a g 398: 14221732 c t  399: 14224920 g a  400: 14228269 g c  401: 14230621c t  402: 14230681 a c  403: 14232644 t a  404: 14233411 c a  405:14234037 t c  406: 14234266 g a  407: 14235064 c a  408: 14235204 c t 409: 14235402 g a  410: 14235813 c t  411: 14236459 a g  412: 14236901g a  413: 14236906 a c  414: 14236958 g t  415: 14237106 c t  416:14237734 a g  417: 14238131 g a  418: 14238784 g a  419: 14238979 a t 420: 14239101 c t  421: 14239346 t c  422: 14239458 g a  423: 14239594a g  424: 14239790 t g  425: 14239876 t c  426: 14240218 c t  427:14240377 t a  428: 14240473 a g  429: 14241088 a g  430: 14241702 a g 431: 14241849 g a  432: 14242333 c t  433: 14243007 a t  434: 14243211g c  435: 14248044 a c  436: 14249184 c g  437: 14251286 g c  438:14255172 g a  439: 14255802 c a  440: 14258178 c t  441: 14259060 g a 442: 14259161 c t  443: 14265514 a g  444: 14266004 g c  445: 14266784a g  446: 14270911 c t  447: 14271868 t c  448: 14273519 a t  449:14275793 c a  450: 14275916 g a  451: 14276093 t c  452: 14276177 a g 453: 14276528 g a  454: 14276897 g a  455: 14276972 t c  456: 14278155a g  457: 14278615 a g  458: 14278692 g a  459: 14279892 g a  460:14280148 g a  461: 14280291 a g  462: 14280782 c t  463: 14281042 a c 464: 14283354 t c  465: 14290678 t c  466: 14290844 a g  467: 14295679c t  468: 14297092 g a  469: 14300848 t c  470: 14303184 t c  471:14303913 a g  472: 14303970 g a  473: 14304669 c g  474: 14305073 t c 475: 14305360 t c  476: 14307893 t c  477: 14308069 c t  478: 14308329a c  479: 14308625 t c  480: 14309321 g a  481: 14309465 g c  482:14310218 g a  483: 14310672 t c  484: 14311035 a g  485: 14311228 t c 486: 14311491 g a  487: 14311865 c t  488: 14312093 a t  489: 14312165g t  490: 14312256 a g  491: 14312275 t c  492: 14312321 a t  493:14312797 g a  494: 14313371 t c  495: 14313671 c t  496: 14313711 g a 497: 14315626 c t  498: 14317417 g a  499: 14317572 t c  500: 14317812c g  501: 14318978 t a  502: 14319024 a g  503: 14319433 g a  504:14319634 g a  505: 14319797 c g  506: 14320165 a g  507: 14320692 c a 508: 14320813 c t  509: 14320844 t g  510: 14321619 a g  511: 14322052a g  512: 14322154 a g  513: 14322220 a g  514: 14323488 c t  515:14323680 c t  516: 14323863 c a  517: 14323972 t c  518: 14324040 a t 519: 14325197 a g  520: 14325540 a g  521: 14329541 t c  522: 14331105c t  523: 14338523 a c  524: 14339636 g c  525: 14340427 c t  526:14348472 g a  527: 14350385 c t  528: 14350727 g a  529: 14351732 t g 530: 14351887 g a  531: 14352733 c t  532: 14353465 a g  533: 14353545t c  534: 14354282 t a  535: 14354993 t c  536: 14355347 c t  537:14355495 c a  538: 14356310 g a  539: 14357040 a g  540: 14357331 g a 541: 14359127 g a  542: 14363514 g a  543: 14367075 c t  544: 14368787g t  545: 14373239 t c  546: 14373986 t g  547: 14375753 t c  548:14375760 g a  549: 14375831 a c  550: 14376454 c g  551: 14376567 g a 552: 14376808 t a  553: 14377209 g a  554: 14377288 g a  555: 14377353g t  556: 14378276 g a  557: 14378370 c t  558: 14379197 a g  559:14395036 a c  560: 14395259 g a  561: 14395598 a g  562: 14395625 c t 563: 14395690 t g  564: 14395722 t c  565: 14395818 g c  566: 14395870t c  567: 14395902 a t  568: 14395954 g a  569: 14396424 g a  570:14397242 t c  571: 14397529 c t  572: 14398288 t g  573: 14398896 g c 574: 14399028 c t  575: 14399757 a g  576: 14399925 t g  577: 14400367c a  578: 14400745 g a  579: 14401434 a c  580: 14401454 g a  581:14402273 c a  582: 14402935 t c  583: 14403897 g c  584: 14405247 c a 585: 14405732 c t  586: 14407060 a t  587: 14407160 t c  588: 14412731g a  589: 14413737 c a  590: 14414482 c t  591: 14414726 g a  592:14417171 t c  593: 14417396 c a  594: 14417433 g t  595: 14417477 c t 596: 14418160 c t  597: 14419575 t c  598: 14420742 t c  599: 14421092a g  600: 14421138 t g  601: 14422812 a t  602: 14424569 g a  603:14424712 t g  604: 14427528 g a  605: 14434249 a g  606: 14434697 g a 607: 14437186 t c  608: 14437221 t g  609: 14438332 t c  610: 14438364t g  611: 14438686 t c  612: 14438954 g a  613: 14439018 t c  614:14439260 t c  615: 14440001 c t  616: 14443243 c t  617: 14446477 c t 618: 14447783 g a  619: 14447829 t a  620: 14448561 c g  621: 14449993c a  622: 14453820 a g  623: 14455156 c t  624: 14458430 g a  625:14462774 a c  626: 14464432 g c  627: 14465972 t c  628: 14466544 a c 629: 14466865 a g  630: 14477623 g t  631: 14479073 t a  632: 14479413a g  633: 14483845 c t  634: 14484193 t c  635: 14485018 t c  636:14500633 a g  637: 14501053 a g  638: 14501214 g t  639: 14505546 c t 640: 14507257 c t  641: 14507719 a g  642: 14507822 c g  643: 14508413a t  644: 14508697 g a  645: 14509951 c t  646: 14511271 c t  647:14512196 g a  648: 14513266 t c  649: 14514848 c t  650: 14516734 c t 651: 14517397 c t  652: 14517691 t c  653: 14519222 c t  654: 14519896c t  655: 14525005 g c  656: 14528986 g c  657: 14529523 g c  658:14530483 t c  659: 14531846 c a  660: 14532854 g a  661: 14534505 c a 662: 14535097 g a  663: 14539337 g c  664: 14540886 g a  665: 14542312t c  666: 14545961 g c  667: 14546904 t c  668: 14546926 g a  669:14549011 g a  670: 14556845 g t  671: 14558860 a g  672: 14560480 a g 673: 14561574 c t  674: 14573065 a c  675: 14574488 a g  676: 14574929t a  677: 14581074 g a  678: 14586576 c g  679: 14588231 g t  680:14588677 a t  681: 14591087 a t  682: 14594493 c t  683: 14598453 c g 684: 14600129 c t  685: 14601491 g c  686: 14603502 g a  687: 14603668t a  688: 14609395 t c  689: 14610858 g a  690: 14615168 t c  691:14615291 a g  692: 14616327 g a  693: 14618602 g a  694: 14618604 g a 695: 14618892 c t  696: 14619088 g a  697: 14621021 t c  698: 14621080a g  699: 14621596 c a  700: 14626694 g a  701: 14627326 t c  702:14627496 t c  703: 14627573 g a  704: 14627856 c t  705: 14628410 a c 706: 14628606 t c  707: 14628943 g t  708: 14630897 a g  709: 14631416c a  710: 14631564 t c  711: 14631874 c g  712: 14632569 c t  713:14633168 g t  714: 14633809 t c  715: 14635240 t g  716: 14637360 a g 717: 14637499 a t  718: 14638334 a g  719: 14638554 g a  720: 14638696t c  721: 14639083 g a  722: 14639418 c t  723: 14639424 t a  724:14640672 g c  725: 14640709 g c  726: 14640930 a c  727: 14640953 a g 728: 14641901 a g  729: 14641976 g a  730: 14642051 c t  731: 14642174g a  732: 14642247 t a  733: 14642286 a g  734: 14642392 t c  735:14642614 c t  736: 14642775 a c  737: 14642852 c t  738: 14644032 c g 739: 14644292 c t  740: 14644589 c a  741: 14644653 g a  742: 14645037c t  743: 14645885 c g  744: 14646291 c t  745: 14646415 g a  746:14647137 c t  747: 14649329 g a  748: 14649396 t c  749: 14649442 g a 750: 14649469 a g  751: 14649532 a c  752: 14649566 t c  753: 14649661c t  754: 14649855 t c  755: 14650183 t c  756: 14650197 g a  757:14650588 a g  758: 14650730 g a  759: 14650852 g c  760: 14651277 g t 761: 14651335 a g  762: 14651435 t c  763: 14651847 c t  764: 14652004g a  765: 14652162 c t  766: 14652276 a g  767: 14652452 t c  768:14652474 c t  769: 14652694 g a  770: 14653708 t c  771: 14654235 a g 772: 14661002 a g  773: 14662594 g a  774: 14663947 a g  775: 14664293t c  776: 14667946 a g  777: 14668382 c g  778: 14677906 a g  779:14677931 g t  780: 14683355 a g  781: 14683707 a g  782: 14683953 g c 783: 14685321 t c  784: 14685566 g a  785: 14685682 g a  786: 14685868a g  787: 14686114 a g  788: 14686396 t c  789: 14686751 c t  790:14686876 c t  791: 14687010 g a  792: 14687213 a t  793: 14689122 t c 794: 14689887 a c  795: 14690010 g a  796: 14690527 c t  797: 14690707t c  798: 14693607 g a  799: 14694039 t c  800: 14694137 t c  801:14694226 a g  802: 14695601 a g  803: 14697255 t c  804: 14697625 t c 805: 14698201 a g  806: 14702430 a g  807: 14703794 t g  808: 14707050g a  809: 14708403 g a  810: 14709040 c a  811: 14713360 t c  812:14713782 c t  813: 14715259 t g  814: 14715324 t c  815: 14715436 c t 816: 14715840 t a  817: 14716796 t a  818: 14716938 t a  819: 14717692a t  820: 14720670 t g  821: 14720870 a g  822: 14720958 a g  823:14721377 g t  824: 14721393 c g  825: 14723843 g c  826: 14724043 c t 827: 14724396 a g  828: 14735736 c t  829: 14746369 g a  830: 14747341c t  831: 14747564 t c  832: 14749491 g t  833: 14751000 g a  834:14752476 a g  835: 14755501 g a  836: 14757128 a t  837: 14758013 a g 838: 14760186 a g  839: 14761259 t c  840: 14761655 a g  841: 14761848c t  842: 14762060 c t  843: 14762610 c t  844: 14763252 a g  845:14763339 t g  846: 14763358 c t  847: 14764385 c t  848: 14764832 g a 849: 14766118 c t  850: 14766695 c g  851: 14767381 c t  852: 14767448g t  853: 14767691 g t  854: 14768282 a c  855: 14768485 a g  856:14769892 c t  857: 14775735 g t  858: 14778167 a g  859: 14778548 g a 860: 14780565 g a  861: 14782481 c t  862: 14783170 t c  863: 14783238g a  864: 14783528 c t  865: 14789648 g c  866: 14789869 a g  867:14792310 a g  868: 14793132 a g  869: 14793358 c t  870: 14794571 c t 871: 14794694 g a  872: 14795297 g c  873: 14795613 t g  874: 14800961c t  875: 14801290 a g  876: 14806680 c t  877: 14806780 g t  878:14808807 g a  879: 14812321 c t  880: 14815234 t g  881: 14815292 a g 882: 14826491 g a  883: 14826755 g c  884: 14827063 t g  885: 14827326g a  886: 14828570 a t  887: 14828644 t a  888: 14830149 c t  889:14830865 c a  890: 14832282 t c  891: 14837049 t g  892: 14837309 t g 893: 14839377 a g  894: 14839380 c g  895: 14839479 c a  896: 14840370a g  897: 14841070 a g  898: 14841947 g c  899: 14844054 c a  900:14844695 g t  901: 14847684 g a  902: 14856106 a c  903: 14856305 g c 904: 14881867 c a  905: 14881913 c g  906: 14883268 c g  907: 14883463c t  908: 14883496 a c  909: 14884123 a g  910: 14885200 t c  911:14886115 a g  912: 14889393 a g  913: 14890241 t c  914: 14890955 a c 915: 14891235 g t  916: 14891547 g a  917: 14893013 g a  918: 14897516a g  919: 14897784 c t  920: 14898476 c t  921: 14898703 t g  922:14899985 g a  923: 14900173 t c  924: 14900736 g t  925: 14901418 c t 926: 14902815 g a  927: 14903113 c a  928: 14903529 c t  929: 14904378g a  930: 14906025 t g  931: 14907342 t c  932: 14907394 a c  933:14907419 c a  934: 14907479 t c  935: 14907742 a g  936: 14916208 a g 937: 14916813 c t  938: 14916928 t c  939: 14917091 g a  940: 14917492t c  941: 14917583 g a  942: 14918606 a g  943: 14919603 c t  944:14921284 t c  945: 14921968 g a  946: 14925699 a g  947: 14927086 g t 948: 14927511 g t  949: 14927761 a g  950: 14930449 c t  951: 14932928g t  952: 14934064 g a  953: 14934220 a t  954: 14934405 c g  955:14935053 g a  956: 14936874 c t  957: 14937239 a g  958: 14938600 a g 959: 14938812 t c  960: 14938839 c t  961: 14939511 t g  962: 14946414t c  963: 14947066 a t  964: 14948931 a g  965: 14949714 g a  966:14949860 t g  967: 14950617 c t  968: 14955687 c t  969: 14957284 a g 970: 14957361 t c  971: 14957636 c t  972: 14962229 a t  973: 14962364g c  974: 14962869 a g  975: 14962889 c c  976: 14962958 c c  977:14963125 c t  978: 14963174 a c  979: 14963729 c c  980: 14964357 a c 981: 14964447 c c  982: 14965500 c c  983: 14966506 g a  984: 14967947c g  985: 14967998 c t  986: 14968368 g a  987: 14968428 t c  988:14968442 c g  989: 14968847 t c  990: 14968966 c t  991: 14969157 g c 992: 14969298 c a  993: 14970379 t c  994: 14970418 g a  995: 14971526c t  996: 14971688 c g  997: 14971772 g a  998: 14973076 g a  999:14973499 c a 1000: 14973824 g c 1001: 14973949 t g 1002: 14974011 t c1003: 14974148 g a 1004: 14974260 t c 1005: 14974378 a g 1006: 14974460t c 1007: 14982560 a g 1008: 14983098 a c 1009: 14983702 a g 1010:14984246 g t 1011: 14984593 a g 1012: 14984596 c t 1013: 14985092 a c1014: 14985239 t c 1015: 14986242 c g 1016: 14986505 t g 1017: 14999579t c 1018: 14999732 t c 1019: 15000805 t c 1020: 15001015 c g 1021:15001541 t c 1022: 15003015 t c 1023: 15003295 c t 1024: 15003506 c a1025: 15003702 t g 1026: 15004887 a t 1027: 15005096 c g 1028: 15005343t c 1029: 15005979 g t 1030: 15006994 a t 1031: 15012376 g c 1032:15012478 c t 1033: 15013750 a g 1034: 15013958 c t 1035: 15014963 g a1036: 15016330 a g 1037: 15017158 g a 1038: 15017812 t c 1039: 15018193t c 1040: 15018598 c t 1041: 15019575 t c 1042: 15020203 t c 1043:15020215 a g 1044: 15020761 c t 1045: 15021675 g a 1046: 15024870 a c1047: 15027668 a g 1048: 15028233 a t 1049: 15030226 t c 1050: 15030777c t 1051: 15031770 a c 1052: 15031862 a g 1053: 15032108 t c 1054:15032579 g a 1055: 15042603 c g 1056: 15042663 g a 1057: 15043235 a g1058: 15044312 c t 1059: 15044487 g c 1060: 15044714 g a 1061: 15044802c t 1062: 15044846 g c 1063: 15045769 t c 1064: 15046216 g t 1065:15047935 t c 1066: 15048235 g a 1067: 15049641 g a 1068: 15052050 a c1069: 15052308 g c 1070: 15052666 g t 1071: 15052897 t g 1072: 15053077c t 1073: 15053098 g a 1074: 15053372 g t 1075: 15053906 a g 1076:15053965 g a 1077: 15054237 t g 1078: 15054358 g t 1079: 15054369 a t1080: 15054413 a g 1081: 15054623 c t 1082: 15055285 a g 1083: 15056247t c 1084: 15056262 c a 1085: 15056524 c g 1086: 15056732 t g 1087:15057645 c t 1088: 15057911 a g 1089: 15059081 t c 1090: 15059227 t c1091: 15059251 g t 1092: 15059355 t c 1093: 15059511 a g 1094: 15059676g c 1095: 15059704 g c 1096: 15061168 a c 1097: 15061851 a g 1098:15062050 a c 1099: 15062336 a c 1100: 15062876 t c 1101: 15062902 c t1102: 15063240 c t 1103: 15063278 g c 1104: 15063388 t c 1105: 15063738t c 1106: 15063889 g a 1107: 15064072 t c 1108: 15064135 c t 1109:15064449 c t 1110: 15064468 t c 1111: 15064803 t g 1112: 15064825 a g1113: 15083316 g t 1114: 15083539 a c 1115: 15085015 a g 1116: 15087382c t 1117: 15087549 c t 1118: 15087811 a c 1119: 15088024 g a 1120:15088408 c t 1121: 15089510 c t 1122: 15090351 a g 1123: 15091082 g a1124: 15091800 c g 1125: 15091818 g c 1126: 15091931 t c 1127: 15092491c t 1128: 15092600 c t 1129: 15093766 t g 1130: 15094258 c t 1131:15095449 t c 1132: 15096410 g c 1133: 15096417 t c 1134: 15097205 t a1135: 15099623 a g 1136: 15100929 a g 1137: 15102290 a g 1138: 15102639t c 1139: 15103451 g a 1140: 15103501 t a 1141: 15103594 g c 1142:15103649 t c 1143: 15103944 g c 1144: 15104691 c t 1145: 15105602 c t1146: 15105975 t c 1147: 15108357 g a 1148: 15112061 g c 1149: 15113179g c 1150: 15113322 a t 1151: 15113753 t c 1152: 15113838 c a 1153:15113882 c t 1154: 15113898 t c 1155: 15114339 c t 1156: 15114389 a g1157: 15114648 g a 1158: 15114880 a g 1159: 15114984 c t 1160: 15114985g a 1161: 15115208 g c 1162: 15115270 g t 1163: 15115470 a g 1164:15115656 g a 1165: 15115762 g c 1166: 15115798 t c 1167: 15115868 a g1168: 15115872 c g 1169: 15116056 a c 1170: 15116070 t g 1171: 15116562c t 1172: 15117228 g a 1173: 15117343 g a 1174: 15117378 t c 1175:15117616 g c 1176: 15118147 t a 1177: 15118222 a g 1178: 15118294 c t1179: 15118320 c a 1180: 15118721 a c 1181: 15118824 g a 1182: 15119382g t 1183: 15120030 t a 1184: 15120282 t c 1185: 15120655 c t 1186:15120709 a c 1187: 15121042 g t 1188: 15121068 a g 1189: 15121138 c t1190: 15121152 c a 1191: 15121365 t c 1192: 15121476 c t 1193: 15121504a g 1194: 15121563 g a 1195: 15121698 c t 1196: 15121918 a g 1197:15122456 c g 1198: 15122528 g c 1199: 15122576 c t 1200: 15123075 c t1201: 15123299 t c 1202: 15125594 g c 1203: 15129221 a c 1204: 15129277t c 1205: 15129443 t c 1206: 15130654 t c 1207: 15130816 a g 1208:15133882 t g 1209: 15135489 a c 1210: 15137526 t c 1211: 15137760 g a1212: 15137880 t c 1213: 15137947 a g 1214: 15138114 t c 1215: 15140503t c 1216: 15140594 g a 1217: 15143181 t c 1218: 15143437 t g 1219:15143561 g a 1220: 15155635 g c 1221: 15156184 a g 1222: 15156288 g c1223: 15156843 g c 1224: 15156864 c a 1225: 15157266 a g 1226: 15157366a g 1227: 15157750 g a 1228: 15157932 c t 1229: 15158367 t c 1230:15158954 g a 1231: 15159251 a g 1232: 15159681 t g 1233: 15159905 t c1234: 15160103 c g 1235: 15160229 g a 1236: 15160375 a g 1237: 15160747a g 1238: 15161208 a g 1239: 15161296 t c 1240: 15162116 a g 1241:15162818 c g 1242: 15163393 g a 1243: 15163709 a g 1244: 15164061 g t1245: 15164535 a c 1246: 15164606 a g 1247: 15164956 a g 1248: 15165414g t 1249: 15165880 a g 1250: 15166496 a g 1251: 15166944 c t 1252:15170886 g t 1253: 15171082 a c 1254: 15171234 a t 1255: 15171477 t c1256: 15171575 g a 1257: 15172248 c t 1258: 15172591 t c 1259: 15172663c t 1260: 15173690 c g 1261: 15173999 t c 1262: 15174464 c g 1263:15174576 c a 1264: 15174731 g t 1265: 15179847 c g 1266: 15181517 a g1267: 15182912 g a 1268: 15188258 c g 1269: 15188944 c g 1270: 15190568a g 1271: 15193056 c a 1272: 15193235 a c 1273: 15196894 c g 1274:15197392 c g 1275: 15197616 c t 1276: 15198273 a g 1277: 15200470 a g1278: 15201112 c t 1279: 15201163 a g 1280: 15210195 a g 1281: 15210821g a 1282: 15210892 c t 1283: 15211414 t c 1284: 15213038 t c 1285:15213698 a g 1286: 15218585 c t 1287: 15219179 c g 1288: 15219910 t g1289: 15219979 t c 1290: 15220030 c a 1291: 15221507 t c 1292: 15221812a g 1293: 15222360 g c 1294: 15235712 a c 1295: 15236093 g a 1296:15237058 t c 1297: 15237243 t a 1298: 15237826 g a 1299: 15245937 g a1300: 15247814 a c 1301: 15248287 a t 1302: 15248858 a g 1303: 15249464a c 1304: 15249918 g a 1305: 15250861 a g 1306: 15257591 a g 1307:15258299 c g 1308: 15258781 t a 1309: 15259393 g c 1310: 15278236 a g1311: 15278332 g c 1312: 15278864 a g 1313: 15280727 c t 1314: 15281279a g 1315: 15284038 a g 1316: 15286073 t a 1317: 15286767 c t 1318:15287268 g a 1319: 15287757 t c 1320: 15288157 c t 1321: 15290861 a g1322: 15292602 t g 1323: 15292856 a t 1324: 15292946 a t 1325: 15294452t c 1326: 15294619 a g 1327: 15295190 c t 1328: 15295340 c g 1329:15295448 g a 1330: 15295751 a g 1331: 15296044 t c 1332: 15298911 c t1333: 15299701 a g 1334: 15301236 t c 1335: 15301721 a g 1336: 15302795c t 1337: 15304359 c t 1338: 15304768 c t 1339: 15305451 c t 1340:15305499 c t 1341: 15306159 a g 1342: 15307257 c t 1343: 15326402 c g1344: 15327372 g a 1345: 15327854 t c 1346: 15328122 c t 1347: 15329473a g 1348: 15330241 a g 1349: 15330332 c t 1350: 15330473 g a 1351:15330915 a c 1352: 15334013 t a 1353: 15335579 c t 1354: 15335902 g c1355: 15337003 t c 1356: 15337602 c t 1357: 15337928 c t 1358: 15338527g c 1359: 15338830 t c 1360: 15339015 c t 1361: 15339975 g a 1362:15340878 c t 1363: 15340950 c t 1364: 15342242 t c 1365: 15342864 a g1366: 15343377 c a 1367: 15343820 a g 1368: 15343964 g a 1369: 15344149a g 1370: 15344260 a g 1371: 15344700 a c 1372: 15345417 c t 1373:15345590 c t 1374: 15345802 a g 1375: 15345997 g t 1376: 15346966 c t1377: 15347172 t c 1378: 15347358 t g 1379: 15347471 c t 1380: 15347710c t 1381: 15347796 c a 1382: 15347920 a g 1383: 15348439 g c 1384:15348529 c t 1385: 15348906 t c 1386: 15349540 a g 1387: 15350434 c t1388: 15350912 g a 1389: 15357981 g a 1390: 15358427 c t 1391: 15360697a g 1392: 15360917 t c 1393: 15360943 c t 1394: 15363937 a t 1395:15366193 a g 1396: 15366365 a c 1397: 15367309 t c 1398: 15367886 c t1399: 15368346 c a 1400: 15369041 a g 1401: 15369192 c g 1402: 15371582t c 1403: 15371834 g a 1404: 15372859 t a 1405: 15372883 g c 1406:15373382 c t 1407: 15376003 t c 1408: 15376545 g c 1409: 15377765 g a1410: 15377859 t a 1411: 15378300 g t 1412: 15379758 g a 1413: 15380744t c 1414: 15381135 t g 1415: 15381405 t c 1416: 15381459 c t 1417:15381699 g c 1418: 15381786 c t 1419: 15381927 g a 1420: 15383192 t c1421: 15383785 t c 1422: 15385245 t c 1423: 15385354 c a 1424: 15386150c t 1425: 15386401 a g 1426: 15387951 a t 1427: 15387995 c g 1428:15389985 t c 1429: 15390251 a g 1430: 15390643 g a 1431: 15392267 c t1432: 15409236 c t 1433: 15410370 g a 1434: 15410509 g a 1435: 15411476t c 1436: 15412787 t c 1437: 15414565 t c 1438: 15414892 t a 1439:15415790 t c 1440: 15416105 t c 1441: 15416836 c g 1442: 15418302 t c1443: 15419812 t a 1444: 15423572 a t 1445: 15424068 a g 1446: 15425337t a 1447: 15425888 t g 1448: 15427076 c t 1449: 15427774 c t 1450:15428455 c a 1451: 15430737 c t 1452: 15430820 a g 1453: 15430977 a g1454: 15431009 a g 1455: 15431108 g a 1456: 15431384 a g 1457: 15431734t c 1458: 15432013 t g 1459: 15432686 t g 1460: 15437902 c g 1461:15438917 c t 1462: 15439622 g a 1463: 15443427 a t 1464: 15443645 c t1465: 15443857 a g 1466: 15444727 t c 1467: 15450381 g a 1468: 15450655t c 1469: 15451393 a c 1470: 15453228 t c 1471: 15454485 c t 1472:15457603 t c 1473: 15458762 t c 1474: 15460247 c t 1475: 15460565 g a1476: 15462506 a g 1477: 15463003 g a 1478: 15463092 a c 1479: 15464063g c 1480: 15464626 t c 1481: 15464934 t c 1482: 15465284 a c 1483:15467849 t c 1484: 15468390 t g 1485: 15471797 t c 1486: 15472451 c t1487: 15473157 g a 1488: 15473855 c a 1489: 15474519 a g 1490: 15474878a c 1491: 15475161 t g 1492: 15475625 g a 1493: 15476413 t c 1494:15478861 a g 1495: 15479973 t c 1496: 15487398 t c 1497: 15490194 g a1498: 15490358 c a 1499: 15491723 c g 1500: 15495785 c t 1501: 15496171g a 1502: 15496250 a g 1503: 15498854 g c 1504: 15499196 g c 1505:15499256 a c 1506: 15523006 c t 1507: 15523665 a g 1508: 15524016 t c1509: 15527375 a t 1510: 15527457 t a 1511: 15527780 a g 1512: 15529195t c 1513: 15529261 a g 1514: 15529955 t c 1515: 15532781 c t 1516:15533397 g a 1517: 15533879 t c 1518: 15534695 g t 1519: 15535616 g a1520: 15536274 a c 1521: 15536511 c t 1522: 15536677 g a 1523: 15536799c a 1524: 15537359 t g 1525: 15537618 a c 1526: 15537702 g t 1527:15538279 c t 1528: 15538634 c t 1529: 15538756 c t 1530: 15540283 c t1531: 15540330 a t 1532: 15540502 a g 1533: 15540516 c g 1534: 15540890t c 1535: 15541750 t c 1536: 15541758 g a 1537: 15542644 t c 1538:15543464 a g 1539: 15546803 g t 1540: 15551175 c t 1541: 15552203 t c1542: 15552298 c a 1543: 15552852 c g 1544: 15554945 c t 1545: 15556161g t 1546: 15556541 g a 1547: 15563972 c t 1548: 15564801 g a 1549:15566839 c t 1550: 15569911 a g 1551: 15577877 c t 1552: 15578595 c t1553: 15580026 c t 1554: 15580045 t c 1555: 15580175 c t 1556: 15580249a c 1557: 15582161 a g 1558: 15582688 t c 1559: 15582848 c t 1560:15582933 c t 1561: 15586302 a g 1562: 15587858 c g 1563: 15588925 c g1564: 15591800 a t 1565: 15591859 c g 1566: 15600225 c t 1567: 15608114t c 1568: 15608937 g a 1569: 15616547 c t 1570: 15616879 t c 1571:15617219 t g 1572: 15618262 t a 1573: 15618417 c g 1574: 15618515 c t1575: 15620129 g a 1576: 15621865 c t 1577: 15622109 c t 1578: 15637711g a 1579: 15638452 t c 1580: 15638866 a g 1581: 15639437 g c 1582:15642518 a g 1583: 15642674 g a 1584: 15645314 c t 1585: 15648663 c t1586: 15649103 a c 1587: 15654686 a c 1588: 15656541 t c 1589: 15657411g a 1590: 15658739 c t 1591: 15663546 c g 1592: 15663679 a g 1593:15663852 g t 1594: 15663985 g t 1595: 15664082 g c 1596: 15664145 g a1597: 15669261 g a 1598: 15670027 t c 1599: 15670322 t c 1600: 15671011g c 1601: 15673660 g a 1602: 15674299 c t 1603: 15676072 g a 1604:15676310 t g 1605: 15676356 a g 1606: 15676616 c g 1607: 15676688 t c1608: 15677147 c t 1609: 15679492 c t 1610: 15679661 g a 1611: 15681218g c 1612: 15681673 a g 1613: 15682323 a g 1614: 15682327 t a 1615:15682496 t g 1616: 15682558 c t 1617: 15682686 a g 1618: 15682767 t c1619: 15683565 t c 1620: 15684832 g a 1621: 15687108 c g 1622: 15687904t c 1623: 15688284 t c 1624: 15688553 c t 1625: 15689098 g t 1626:15689545 t c 1627: 15690113 a g 1628: 15690137 g a 1629: 15690191 t c1630: 15690624 g a 1631: 15690902 a g 1632: 15691598 c a 1633: 15692228c g 1634: 15692260 c t 1635: 15692271 c t 1636: 15692337 t c 1637:15692526 c t 1638: 15692586 t c 1639: 15692696 g a 1640: 15692747 c t1641: 15692833 t c 1642: 15693076 t g 1643: 15693152 a c 1644: 15693231g a 1645: 15693325 c t 1646: 15693734 a g 1647: 15693746 c t 1648:15694033 t g 1649: 15694052 t c 1650: 15694619 a g 1651: 15694659 t c1652: 15703901 g c 1653: 15707451 a c 1654: 15707939 g c 1655: 15707979g c 1656: 15708291 g a 1657: 15708450 g a 1658: 15709137 c t 1659:15710288 g c 1660: 15710413 t g 1661: 15711217 t c 1662: 15712103 c t1663: 15712240 t c 1664: 15713181 c t 1665: 15713268 c t 1666: 15714196g t 1667: 15714283 c t 1668: 15714821 t c 1669: 15714913 t c 1670:15715978 a c 1671: 15718084 a g 1672: 15718481 c t 1673: 15718631 a c1674: 15718740 a c 1675: 15718816 g a 1676: 15722417 c a 1677: 15724448c g 1678: 15730898 c a 1679: 15731033 c g 1680: 15732704 a g 1681:15733164 g t 1682: 15733187 c t 1683: 15736091 t c 1684: 15736526 g a1685: 15737076 a g 1686: 15739695 a c 1687: 15739891 g a 1688: 15740481c a 1689: 15751366 a g 1690: 15753534 t g 1691: 15756338 c t 1692:15759372 a g 1693: 15762194 c t 1694: 15773733 a g 1695: 15777456 g c1696: 15778730 c t 1697: 15779025 g a 1698: 15783049 a g 1699: 15783412c t 1700: 15799315 g a 1701: 15799533 t c 1702: 15806274 c a 1703:15809218 t c 1704: 15816136 c t 1705: 15817833 c t 1706: 15818484 c t1707: 15819000 c t 1708: 15819001 g a 1709: 15819890 a t 1710: 15820114a g 1711: 15828926 g a 1712: 15829019 g c 1713: 15829255 g t 1714:15830468 a g 1715: 15831550 g t 1716: 15832981 c t 1717: 15834204 a g1718: 15835339 a g 1719: 15836962 c t 1720: 15842893 c t 1721: 15843308a g 1722: 15845674 a g 1723: 15847522 a g 1724: 15848497 a g 1725:15848531 a g 1726: 15849033 g a 1727: 15849827 a g 1728: 15850206 c t1729: 15850845 a t 1730: 15851620 c a 1731: 15852141 c t 1732: 15853572c t 1733: 15853834 c t 1734: 15854287 c t 1735: 15854345 g t 1736:15854383 c t 1737: 15854491 t c 1738: 15854988 a g 1739: 15855036 g a1740: 15856634 t c 1741: 15857906 a g 1742: 15858997 t c 1743: 15874301g a 1744: 15875743 a g 1745: 15887486 t c 1746: 15889701 a g 1747:15890290 t g 1748: 15890995 g t 1749: 15892019 g t 1750: 15896400 t g1751: 15897571 a t 1752: 15899275 t g 1753: 15902578 t g 1754: 15902689g a 1755: 15903864 t g 1756: 15919825 a g 1757: 15931959 a g 1758:15932046 c t 1759: 15932544 t c 1760: 15933606 c t 1761: 15935097 g t1762: 15935241 c t 1763: 15935902 c t 1764: 15936345 a g 1765: 15937676a t 1766: 15937927 g t 1767: 15942035 c g 1768: 15943256 a g 1769:15943625 c a 1770: 15944014 t c 1771: 15983697 g t 1772: 15983783 c t1773: 15984281 a g 1774: 15986236 t a 1775: 15986991 c a 1776: 15988284a c 1777: 15992536 g a 1778: 16008242 a g 1779: 16008657 t g 1780:16009127 t c 1781: 16024511 g c 1782: 16030603 t c 1783: 16030715 t c1784: 16030968 a g 1785: 16037236 c t 1786: 16038317 g a 1787: 16038409c t 1788: 16038497 c t 1789: 16038572 g c 1790: 16039175 g a 1791:16040204 g a 1792: 16041425 c t 1793: 16042095 c t 1794: 16045383 c t1795: 16045823 c t 1796: 16046596 c t 1797: 16047021 a g 1798: 16047262g t 1799: 16052110 t c 1800: 16054857 g a 1801: 16056362 t g 1802:16057875 g t 1803: 16058116 g a 1804: 16058654 g a 1805: 16060655 t g1806: 16061286 a t 1807: 16062047 t c 1808: 16065804 a c 1809: 16067677g t 1810: 16070093 t c 1811: 16070754 t c 1812: 16073742 g a 1813:16075005 g a 1814: 16075669 g a 1815: 16076345 a g 1816: 16077846 g a1817: 16079168 c t 1818: 16080584 a c 1819: 16081158 t c 1820: 16081844g a 1821: 16082851 a g 1822: 16085227 t g 1823: 16087921 g a 1824:16089418 a g 1825: 16098425 a g 1826: 16099068 c t 1827: 16101029 c t1828: 16101238 g a 1829: 16101503 t g 1830: 16101922 t g 1831: 16102747c t 1832: 16103415 a g 1833: 16104748 a t 1834: 16105384 a g 1835:16105646 g t 1836: 16105738 a g 1837: 16106737 a c 1838: 16107103 c t1839: 16107196 g t 1840: 16108455 g t 1841: 16109490 a g 1842: 16109580a g 1843: 16110463 t a 1844: 16110632 c t 1845: 16111189 g a 1846:16111591 a g 1847: 16113216 g t 1848: 16113257 g t 1849: 16113390 a t1850: 16113450 t c 1851: 16113549 c t 1852: 16116286 a t 1853: 16117063a g 1854: 16118964 c t 1855: 16120186 a g 1856: 16122504 a g 1857:16123008 a g 1858: 16123345 c t 1859: 16123364 g t 1860: 16124187 g c1861: 16125749 g t 1862: 16125865 g t 1863: 16126708 t g 1864: 16126807c g 1865: 16128540 a g 1866: 16128689 g t 1867: 16130538 t c 1868:16132743 a g 1869: 16133485 c t 1870: 16136056 g c 1871: 16156909 g a1872: 16159187 c t 1873: 16159236 a g 1874: 16161448 c t 1875: 16162085a g 1876: 16163596 g a 1877: 16164420 g a 1878: 16165307 a g 1879:16166790 a g 1880: 16168106 c t 1881: 16170838 t c 1882: 16172349 t g1883: 16174395 c a 1884: 16176693 a t 1885: 16177280 g a 1886: 16179498a t 1887: 16185288 c t 1888: 16189970 c a 1889: 16190273 a g 1890:16191151 a g 1891: 16192017 a g 1892: 16194730 a c 1893: 16196493 a g1894: 16236531 c t 1895: 16252821 a g 1896: 16258852 c t 1897: 16259538a c 1898: 16260888 c t 1899: 16262068 c t 1900: 16262116 a g 1901:16263909 g t 1902: 16265700 g t 1903: 16271911 a g 1904: 16291109 a g1905: 16291287 c t 1906: 16291786 c t 1907: 16293662 c t 1908: 16294248c t 1909: 16294712 a g 1910: 16297048 a g 1911: 16297346 c t 1912:16297483 c t 1913: 16298444 t c 1914: 16298955 a g 1915: 16299046 a g1916: 16299075 t c 1917: 16303288 a g 1918: 16315275 c a 1919: 16315387c g 1920: 16316186 a c 1921: 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2454: 17187608 t c2455: 17187972 a c 2456: 17188458 t c 2457: 17188792 g a 2458: 17189416c t 2459: 17189438 a g 2460: 17189954 t g 2461: 17190814 c t 2462:17190947 t c 2463: 17190955 a g 2464: 17191095 c t 2465: 17191187 a g2466: 17191319 a c 2467: 17191384 c t 2468: 17191706 c t 2469: 17191828c t 2470: 17191888 a g 2471: 17192125 t c 2472: 17192155 t g 2473:17192291 c t 2474: 17192323 t c 2475: 17192740 a g 2476: 17192956 c a2477: 17193172 g a 2478: 17193312 g a 2479: 17193510 t c 2480: 17193677c t 2481: 17193691 t c 2482: 17194149 a g 2483: 17194278 a g 2484:17194541 a t 2485: 17194598 g a 2486: 17194676 t a 2487: 17197658 a t2488: 17197883 a t 2489: 17197893 a g 2490: 17198390 g c 2491: 17198783a t 2492: 17198890 c t 2493: 17199459 g t 2494: 17200122 t a 2495:17200243 t c 2496: 17201223 a g 2497: 17201302 a g 2498: 17201457 g t2499: 17201481 a t 2500: 17201498 a g 2501: 17203618 g a 2502: 17203703t c 2503: 17203883 c t 2504: 17203980 a g 2505: 17204040 a c 2506:17204101 c t 2507: 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2667: 17402486t a 2668: 17402706 t c 2669: 17403422 g a 2670: 17403569 t c 2671:17407971 t a 2672: 17408763 c t 2673: 17409076 t c 2674: 17410171 c t2675: 17410367 g a 2676: 17410479 a t 2677: 17410778 a g 2678: 17412072t g 2679: 17412874 c g 2680: 17413782 g a 2681: 17415789 a c 2682:17416338 t c 2683: 17416942 c t 2684: 17417116 a t 2685: 17417216 c t2686: 17417458 c t 2687: 17419421 a g 2688: 17422486 c g 2689: 17422680g a 2690: 17425052 g t 2691: 17425744 g t 2692: 17427232 g a 2693:17428886 c t 2694: 17431749 t a 2695: 17432007 c g 2696: 17438436 c t2697: 17438615 t c 2698: 17438849 a g 2699: 17440553 g c 2700: 17440770t c 2701: 17442496 t c 2702: 17442886 a g 2703: 17444799 t g 2704:17447422 a c 2705: 17448013 a g 2706: 17449885 a g 2707: 17454102 t c2708: 17459309 g a 2709: 17459622 a g 2710: 17459786 a g 2711: 17461195t g 2712: 17464114 c t 2713: 17464234 c g 2714: 17467021 a t 2715:17467646 g a 2716: 17468714 g c 2717: 17469263 c t 2718: 17469937 a g2719: 17473605 c t 2720: 17473655 c t 2721: 17473665 a t 2722: 17476466a g 2723: 17477487 c g 2724: 17483080 g a 2725: 17488365 t a 2726:17506367 c t 2727: 17509277 t c 2728: 17509402 a g 2729: 17509738 g a2730: 17510432 g a 2731: 17510712 t c 2732: 17512367 g a 2733: 17513682t c 2734: 17513717 t c 2735: 17513805 a g 2736: 17514142 a g 2737:17514374 g a 2738: 17515443 a c 2739: 17516105 a g 2740: 17516225 a g2741: 17516513 c g 2742: 17517387 g a 2743: 17517712 t c 2744: 17517829c t 2745: 17521626 t c 2746: 17521840 t c 2747: 17521936 t a 2748:17522729 c t 2749: 17524342 c a 2750: 17526995 c t 2751: 17527822 g a2752: 17528701 c t 2753: 17528981 a g 2754: 17532497 c a 2755: 17536364g a 2756: 17536385 c t 2757: 17539592 a t 2758: 17549846 c t 2759:17550048 c g 2760: 17550111 c t 2761: 17550222 t a 2762: 17550391 c t2763: 17550610 g c 2764: 17551171 t c 2765: 17551333 t c 2766: 17552369a g 2767: 17557676 t a 2768: 17559322 c a 2769: 17559640 c t 2770:17562208 g c 2771: 17564241 c a 2772: 17564731 c t 2773: 17565826 t c2774: 17569570 a g 2775: 17571660 c g 2776: 17572368 g a 2777: 17572814g a 2778: 17576282 g a 2779: 17577520 g a 2780: 17578871 t g 2781:17580257 c t 2782: 17580288 t c 2783: 17581052 t c 2784: 17585038 t c2785: 17585627 c t 2786: 17587414 c t 2787: 17590718 a c 2788: 17591876t c 2789: 17593883 t c 2790: 17594527 c t 2791: 17595240 a g 2792:17596333 a g 2793: 17597081 a g 2794: 17597473 t c 2795: 17602743 g a2796: 17602898 g a 2797: 17611242 c t 2798: 17612456 c t 2799: 17613247a g 2800: 17613620 t c 2801: 17613686 t c 2802: 17614407 t c 2803:17614736 g a 2804: 17625088 a g 2805: 17626993 c t 2806: 17629231 g a2807: 17631211 t g 2808: 17631527 t c 2809: 17633594 g a 2810: 17634884g a 2811: 17635348 t g 2812: 17635522 g a 2813: 17637920 t c 2814:17643762 g a 2815: 17644672 t c 2816: 17645925 c t 2817: 17646135 c t2818: 17646248 t a 2819: 17646326 a g 2820: 17646546 g a 2821: 17647096g c 2822: 17647216 g a 2823: 17647454 c t 2824: 17650077 c g 2825:17651490 g t 2826: 17651754 g a 2827: 17652168 g a 2828: 17652686 g c2829: 17653308 a g 2830: 17653504 a g 2831: 17656784 t c 2832: 17656858g a 2833: 17657525 c t 2834: 17657674 g t 2835: 17658409 g a 2836:17659415 g c 2837: 17661175 c t 2838: 17662776 g a 2839: 17662960 a g2840: 17663029 g t 2841: 17663410 c t 2842: 17663451 g a 2843: 17663486g t 2844: 17663630 c g 2845: 17664261 t c 2846: 17664468 t c 2847:17664542 c t 2848: 17664602 c t 2849: 17665201 g a 2850: 17666081 g a2851: 17666248 t c 2852: 17666315 a g 2853: 17666711 a g 2854: 17667126c a 2855: 17667543 a t 2856: 17667614 c t 2857: 17668434 a t 2858:17668940 g t 2859: 17669504 t c 2860: 17669574 a g 2861: 17670408 t c2862: 17670474 g a 2863: 17670565 a g 2864: 17671157 g t 2865: 17671427g a 2866: 17671898 a g 2867: 17673118 g t 2868: 17673199 a t 2869:17673446 t c 2870: 17673674 c t 2871: 17673832 t c 2872: 17675317 g a2873: 17676331 g c 2874: 17676441 g a 2875: 17680205 g a 2876: 17680298c t 2877: 17680378 g c 2878: 17680484 t c 2879: 17680600 g a 2880:17680841 a g 2881: 17680997 a g 2882: 17681574 t c 2883: 17682962 c g2884: 17683317 c a 2885: 17683766 c a 2886: 17684178 a c 2887: 17684698t g 2888: 17684742 c a 2889: 17684934 c g 2890: 17685171 g c 2891:17685301 c t 2892: 17686696 a t 2893: 17688714 g a 2894: 17688720 a g2895: 17694577 a t 2896: 17694726 c g 2897: 17696863 c a 2898: 17698651t c 2899: 17699827 c a 2900: 17705794 a t 2901: 17709695 g a 2902:17720429 a c 2903: 17721954 t c 2904: 17725315 a g 2905: 17727405 c g2906: 17730562 a g 2907: 17736986 c t 2908: 17737860 c t 2909: 17742267a g 2910: 17742564 c t 2911: 17743316 g a 2912: 17745189 a g 2913:17745881 c a 2914: 17747070 c g 2915: 17749146 t c 2916: 17749218 c a2917: 17756821 a g 2918: 17758061 a c 2919: 17760702 g a 2920: 17760780t g 2921: 17760976 a g 2922: 17761185 a t 2923: 17761794 g a 2924:17761811 t g 2925: 17762567 c t 2926: 17762975 c t 2927: 17763485 g a2928: 17764149 t c 2929: 17764437 a t 2930: 17768287 t a 2931: 17771739a g 2932: 17771809 c t 2933: 17773064 c t 2934: 17773377 g a 2935:17775884 t c 2936: 17775964 g a 2937: 17777678 a c 2938: 17778812 t a2939: 17779980 c t 2940: 17781053 a g 2941: 17788387 a t 2942: 17788484g c 2943: 17791361 a g 2944: 17792413 c a 2945: 17794602 t c 2946:17795187 t g 2947: 17795652 a c 2948: 17795980 g a 2949: 17796086 t c2950: 17796688 t c 2951: 17796764 a g 2952: 17796795 c t 2953: 17797812g a 2954: 17799562 t c 2955: 17799732 c t 2956: 17800578 c t 2957:17800679 t c 2958: 17803511 c t 2959: 17804498 a g 2960: 17810832 c t2961: 17812485 c t 2962: 17819555 t a 2963: 17824538 t c 2964: 17828380c t 2965: 17833406 a g 2966: 17833983 c t 2967: 17835269 t c 2968:17836520 g a 2969: 17836781 c g 2970: 17841917 t c 2971: 17843934 t c2972: 17844423 c g 2973: 17847113 a g 2974: 17850031 g a 2975: 17852052c g 2976: 17855415 c t 2977: 17858294 a c 2978: 17864141 g t 2979:17865880 a g 2980: 17867102 a g 2981: 17872103 c t 2982: 17872957 t c2983: 17873857 a c 2984: 17885094 c g 2985: 17887099 t c 2986: 17888521t c 2987: 17902559 c a 2988: 17902569 a g 2989: 17902876 g a 2990:17903104 g a 2991: 17903222 c t 2992: 17903743 t a 2993: 17903827 t c2994: 17904859 t c 2995: 17905021 g a 2996: 17905668 a t 2997: 17905975c g 2998: 17908674 g t 2999: 17909256 t c 3000: 17911473 c a 3001:17911594 c g 3002: 17912462 t g 3003: 17912827 t c 3004: 17912924 c t3005: 17913950 a g 3006: 17914144 t c 3007: 17915236 c t 3008: 17920938g a 3009: 17921268 c t 3010: 17921350 t c 3011: 17921369 c t 3012:17933425 c t 3013: 17935057 c t 3014: 17935888 c t 3015: 17937617 c g3016: 17938723 a c 3017: 17939084 g a 3018: 17939115 t c 3019: 17939742a g 3020: 17939986 c a 3021: 17941403 g c 3022: 17941840 t c 3023:17942620 g a 3024: 17943731 t g 3025: 17943777 t c 3026: 17955426 t c3027: 17956818 a g 3028: 17966204 c t 3029: 17968513 c g 3030: 17969043a g 3031: 17969075 g t 3032: 17970354 c t 3033: 17972629 a g 3034:17973274 g a 3035: 17974892 g t 3036: 17978997 g a 3037: 17983505 g a3038: 17983822 c t 3039: 17987325 a g 3040: 17988096 t c 3041: 17991260t c 3042: 17991844 g a 3043: 17991933 c a 3044: 17991961 t g 3045:17992340 c t 3046: 17992669 c t 3047: 17994812 g c 3048: 17995075 t c3049: 17995757 a g 3050: 17996222 c t 3051: 17996520 t g 3052: 17997406g c 3053: 17998464 a c 3054: 17999408 g t 3055: 17999483 a c 3056:17999616 g a 3057: 17999790 a g 3058: 18000063 c t 3059: 18000103 t c3060: 18000178 g a 3061: 18001339 g a 3062: 18001405 t c 3063: 18002501c t 3064: 18003768 a g 3065: 18004013 a c 3066: 18004040 t c 3067:18004202 g t 3068: 18004308 c t 3069: 18004507 c t 3070: 18004554 a t3071: 18004573 t c 3072: 18004627 g a 3073: 18004806 a g 3074: 18004945c t 3075: 18004989 g a 3076: 18005122 c t 3077: 18005896 t c 3078:18006127 t c 3079: 18006206 a g 3080: 18006260 g t 3081: 18006365 t c3082: 18006954 c t 3083: 18007031 c t 3084: 18007042 a g 3085: 18007187t c 3086: 18007515 a g 3087: 18007521 a t 3088: 18007703 a g 3089:18007737 c t 3090: 18007825 g a 3091: 18011843 a c 3092: 18021152 a g3093: 18021191 g a 3094: 18021303 g a 3095: 18021524 a c 3096: 18022707a t 3097: 18025392 g a 3098: 18030997 t c 3099: 18033814 g a 3100:18033962 g a 3101: 18064060 c t 3102: 18064455 c t 3103: 18064623 c t3104: 18066263 a g 3105: 18066463 c t 3106: 18066998 c t 3107: 18067103t a 3108: 18067290 g a 3109: 18069198 t c 3110: 18069910 g a 3111:18070164 g a 3112: 18072572 g a 3113: 18072925 t c 3114: 18074338 c t3115: 18074380 a c 3116: 18074455 c t 3117: 18075694 g a 3118: 18076179a g 3119: 18076283 a g 3120: 18076338 g a 3121: 18080048 a g 3122:18081695 a g 3123: 18082352 c t 3124: 18083163 t c 3125: 18084356 c t3126: 18086551 a g 3127: 18086717 c t 3128: 18087120 a g 3129: 18087431t c 3130: 18087675 c t 3131: 18087828 g t 3132: 18087883 a g 3133:18088892 a g 3134: 18089833 t c 3135: 18090029 a g 3136: 18091780 a g3137: 18093344 c t 3138: 18094667 g t 3139: 18098102 t c 3140: 18102051g a 3141: 18103547 c g 3142: 18103621 t a 3143: 18105666 a g 3144:18112452 a g 3145: 18113119 g a 3146: 18114308 g a 3147: 18125288 t c3148: 18129336 g a 3149: 18134303 g c 3150: 18137041 g t 3151: 18138481g a 3152: 18138871 a g 3153: 18141716 g c 3154: 18142013 t c 3155:18142482 a g 3156: 18142498 g a 3157: 18143539 a g 3158: 18144507 g a3159: 18146381 a g 3160: 18147285 a g 3161: 18147368 g a 3162: 18147479t g 3163: 18147849 t g 3164: 18148090 a g 3165: 18148391 g t 3166:18149727 a t 3167: 18162515 c t 3168: 18167850 a c 3169: 18169299 c t3170: 18170395 g a

[0024] TABLE 2 POSITION REFERENCE_BASE ALTERNATE_BASE  1: 13786332 g c 2: 13789552 t c  3: 13794088 g t  4: 13795042 t g  5: 13795784 g c  6:13798031 a g  7: 13798945 g a  8: 13808775 g t  9: 13810343 t a  10:13845012 t g  11: 13857670 t a  12: 13863248 a g  13: 13868547 c g  14:13871664 g a  15: 13872007 t g  16: 13944350 t a  17: 13946958 c t  18:13952218 g a  19: 13952240 c t  20: 13953249 c t  21: 13955300 a g  22:13955542 a g  23: 13957524 c t  24: 13969607 g a  25: 13989352 c t  26:13991942 t c  27: 13994180 a g  28: 13998796 c t  29: 14012310 a c  30:14022029 c t  31: 14055038 g a  32: 14056661 a g  33: 14057058 c t  34:14057841 a g  35: 14063842 t c  36: 14064036 a g  37: 14065022 a c  38:14065054 a g  39: 14072304 t c  40: 14077207 c t  41: 14089145 t c  42:14092446 c t  43: 14109164 t c  44: 14136408 t a  45: 14152957 a g  46:14154909 c t  47: 14163567 g c  48: 14202814 a g  49: 14202816 g a  50:14203860 t c  51: 14227826 c t  52: 14233001 g t  53: 14246775 a g  54:14249388 g a  55: 14251065 g c  56: 14253526 t c  57: 14282614 c t  58:14289973 g t  59: 14303801 a t  60: 14305564 g a  61: 14308745 a g  62:14309271 g a  63: 14313634 c a  64: 14316517 t c  65: 14336497 a g  66:14337704 t c  67: 14341977 c g  68: 14344127 a c  69: 14344521 t g  70:14347249 c t  71: 14348761 g a  72: 14356012 t g  73: 14357072 t g  74:14368727 c t  75: 14380858 c t  76: 14381653 a g  77: 14412471 g c  78:14443836 c a  79: 14450249 t a  80: 14523926 a g  81: 14529213 t c  82:14560271 g a  83: 14591293 g a  84: 14601683 t c  85: 14614643 t c  86:14627536 c a  87: 14639294 c t  88: 14639798 c t  89: 14666163 t c  90:14686785 c t  91: 14778389 t a  92: 14791193 t g  93: 14806046 t g  94:14808476 a g  95: 14808794 g a  96: 14809810 c t  97: 14809974 c t  98:14814482 g a  99: 14814537 t a 100: 14823503 g t 101: 14825824 t c 102:14826425 g a 103: 14827550 c t 104: 14834456 c g 105: 14842048 t c 106:14886344 g t 107: 14890054 a c 108: 14892017 c t 109: 14892649 c t 110:14900671 a t 111: 14945268 t c 112: 14946296 a g 113: 14951614 a g 114:14951808 c g 115: 14957690 c a 116: 14965613 c t 117: 14970970 g a 118:14999022 g a 119: 14999072 a c 120: 14999132 t g 121: 14999231 a g 122:14999774 c t 123: 14999842 t g 124: 15000185 c a 125: 15000225 t a 126:15000615 g a 127: 15000928 g c 128: 15001303 c t 129: 15001357 a c 130:15001514 c g 131: 15001760 g a 132: 15001785 g a 133: 15001983 a g 134:15002044 c t 135: 15002118 t c 136: 15002260 g c 137: 15002436 g c 138:15002447 a g 139: 15002601 a g 140: 15002681 a g 141: 15003106 c g 142:15003363 g t 143: 15003544 c a 144: 15003596 t c 145: 15003973 g t 146:15004000 c t 147: 15004200 g a 148: 15004222 t g 149: 15004468 t c 150:15004577 g a 151: 15004725 a t 152: 15004739 t c 153: 15004935 g c 154:15004988 c t 155: 15005084 g a 156: 15005148 a g 157: 15005159 a g 158:15005540 g a 159: 15025974 t c 160: 15026705 a c 161: 15048712 a g 162:15087229 g a 163: 15115597 c a 164: 15141829 a g 165: 15143231 g a 166:15210898 g t 167: 15232784 c t 168: 15249147 t a 169: 15286306 t c 170:15298032 t c 171: 15299313 g t 172: 15335133 c t 173: 15351079 a t 174:15362167 t g 175: 15370212 a g 176: 15373919 t c 177: 15374182 a g 178:15375609 a t 179: 15376324 t a 180: 15395417 t c 181: 15399434 c t 182:15414814 a t 183: 15423539 t c 184: 15424699 a t 185: 15427464 t g 186:15435332 t c 187: 15437951 a g 188: 15438194 t c 189: 15453738 a c 190:15471061 t c 191: 15522640 a c 192: 15553225 a g 193: 15555505 c t 194:15565145 a g 195: 15617474 t c 196: 15642114 a g 197: 15679735 t g 198:15696652 t c 199: 15708909 t c 200: 15711358 g a 201: 15742331 t c 202:15745340 c g 203: 15792778 c t 204: 15809741 a g 205: 15813986 c t 206:15814037 a g 207: 15815872 g a 208: 15815917 t c 209: 15817984 t c 210:15818374 a g 211: 15849570 a c 212: 15857950 a t 213: 15865992 t a 214:15881133 g c 215: 15887520 t c 216: 15895527 g c 217: 15903809 a t 218:15922876 g a 219: 15937899 c t 220: 15949824 c t 221: 15954079 t c 222:15955158 a g 223: 15970406 t c 224: 15978044 g a 225: 16029704 a g 226:16030927 t c 227: 16035195 a g 228: 16038904 g c 229: 16056870 c t 230:16094042 t g 231: 16094737 a t 232: 16104503 c t 233: 16161202 c t 234:16168166 c g 235: 16171036 g a 236: 16173907 t g 237: 16193590 a g 238:16217867 t c 239: 16238199 c t 240: 16243372 a t 241: 16274234 a g 242:16317969 a g 243: 16327992 g c 244: 16337850 a t 245: 16338022 t g 246:16360523 t c 247: 16389837 g a 248: 16394347 t c 249: 16394992 a g 250:16403291 g t 251: 16405553 a g 252: 16429877 a g 253: 16431582 t c 254:16434635 a g 255: 16437778 g t 256: 16439992 c g 257: 16447097 t c 258:16491522 a g 259: 16494732 t g 260: 16501248 a g 261: 16508146 t c 262:16636222 t c 263: 16636797 c a 264: 16686966 c t 265: 16705428 c t 266:16753307 a t 267: 16757962 a g 268: 16766335 c t 269: 16779020 a t 270:16784770 c t 271: 16803656 c g 272: 16804768 g t 273: 16853980 c t 274:16858486 a t 275: 16861847 c t 276: 16865089 a c 277: 16866854 c g 278:16876526 t c 279: 16883444 c t 280: 16968693 t c 281: 16971929 a g 282:17021105 g a 283: 17031548 t c 284: 17060994 t c 285: 17064711 c t 286:17064940 a g 287: 17074484 c t 288: 17088556 c t 289: 17113095 a g 290:17116558 a c 291: 17120029 a g 292: 17131193 t c 293: 17153912 a g 294:17167383 t c 295: 17170539 g c 296: 17179698 a t 297: 17193632 g a 298:17199522 a t 299: 17201025 t a 300: 17207642 c t 301: 17228878 g a 302:17232783 a g 303: 17233396 g a 304: 17238359 a g 305: 17239125 g a 306:17243006 c t 307: 17244215 g c 308: 17244585 g a 309: 17245498 g c 310:17249409 c t 311: 17258945 g a 312: 17259285 a g 313: 17262233 g t 314:17265233 g a 315: 17267396 a t 316: 17276911 g a 317: 17283143 g a 318:17287690 a t 319: 17296703 g c 320: 17316277 g a 321: 17322467 a c 322:17345540 g t 323: 17351785 a c 324: 17381722 g a 325: 17437280 g c 326:17467870 t c 327: 17468444 a g 328: 17490372 g a 329: 17548337 g t 330:17615441 g c 331: 17627574 a c 332: 17635725 a c 333: 17645927 a g 334:17646932 t c 335: 17683823 t g 336: 17711750 c g 337: 17776065 a g 338:17779015 a g 339: 17819480 a g 340: 17820025 t c 341: 17887100 t a 342:17902653 a t 343: 17902971 t c 344: 17902973 a g 345: 17975014 g c 346:18003363 a g 347: 18006481 a t 348: 18015976 t c 349: 18016117 g a 350:18018984 t g 351: 18022010 t c 352: 18023585 c t 353: 18023870 g a 354:18025742 g c 355: 18075838 g c 356: 18134065 c t 357: 18151118 g a 358:18156425 a t 359: 18166871 g c 360: 18167968 a g 361: 18170580 c t

[0025] TABLE 3 POSITION REFERENCE_BASE ALTERNATE_BASE  1: 13793202 c t 2: 13795971 g a  3: 13807082 a c  4: 13807169 t c  5: 13807650 t c  6:13809615 c t  7: 13809703 c t  8: 13812148 c t  9: 13833651 c t  10:13840293 c a  11: 13851092 c t  12: 13858215 g a  13: 13860247 c t  14:13861613 a g  15: 13862837 c t  16: 13868013 c g  17: 13868860 a g  18:13869319 a g  19: 13899997 c a  20: 13901998 c g  21: 13918642 t c  22:13918743 g a  23: 13925431 t g  24: 13939753 a t  25: 13954707 a g  26:13968279 t c  27: 13989194 t c  28: 13994402 a g  29: 14027813 t c  30:14028654 a g  31: 14029967 a c  32: 14031277 g a  33: 14032871 g c  34:14034217 g a  35: 14034364 t c  36: 14046782 c t  37: 14051729 t c  38:14052410 t c  39: 14062535 a g  40: 14062927 c t  41: 14065683 a c  42:14068709 a c  43: 14079109 a g  44: 14089137 a c  45: 14089142 a g  46:14095378 a g  47: 14109422 g a  48: 14122001 a c  49: 14141359 a c  50:14142005 t g  51: 14142139 a c  52: 14155080 a t  53: 14201941 t g  54:14203698 c t  55: 14203930 a g  56: 14204116 t c  57: 14218571 a t  58:14224397 t c  59: 14228263 g c  60: 14235135 c t  61: 14241206 c t  62:14244972 g a  63: 14249399 a g  64: 14251146 g c  65: 14251892 t c  66:14253621 a t  67: 14254529 t a  68: 14277524 a g  69: 14279513 t a  70:14289715 t a  71: 14290282 a g  72: 14290530 g t  73: 14294997 t c  74:14295769 c t  75: 14295939 a g  76: 14297189 t c  77: 14299671 a g  78:14299674 c t  79: 14299711 t c  80: 14300125 c t  81: 14304391 a g  82:14304642 t c  83: 14307883 t c  84: 14308299 a g  85: 14308460 g a  86:14310283 c t  87: 14312072 a g  88: 14315594 t c  89: 14325463 t g  90:14325687 g t  91: 14336793 g a  92: 14351418 g a  93: 14351691 g c  94:14352181 c t  95: 14354527 t c  96: 14355445 c g  97: 14361735 g a  98:14362906 t c  99: 14377173 t c 100: 14379074 a c 101: 14379466 c t 102:14392496 t c 103: 14392568 g a 104: 14395584 a c 105: 14396231 c t 106:14412774 a g 107: 14424801 t c 108: 14427417 t c 109: 14427482 g c 110:14440576 c a 111: 14442675 t g 112: 14442719 t g 113: 14444533 a g 114:14446001 a g 115: 14448003 t a 116: 14449153 c t 117: 14454279 t g 118:14459068 c t 119: 14464047 a t 120: 14464959 t c 121: 14465766 t c 122:14475385 t c 123: 14500484 c t 124: 14514847 c t 125: 14520160 a t 126:14525178 a c 127: 14529211 c t 128: 14532728 t c 129: 14536062 a c 130:14541497 a g 131: 14544386 t c 132: 14581049 t c 133: 14583783 c a 134:14584821 c g 135: 14605448 c t 136: 14621113 t c 137: 14621379 t a 138:14623460 a g 139: 14630525 a c 140: 14630610 t g 141: 14631799 t c 142:14632590 t c 143: 14641424 a t 144: 14644530 a t 145: 14645138 c t 146:14646515 c t 147: 14671181 a g 148: 14672513 t g 149: 14673701 t c 150:14676902 c t 151: 14704141 t a 152: 14708401 a g 153: 14759724 t c 154:14775795 c a 155: 14778736 g a 156: 14801146 c t 157: 14834449 c g 158:14836432 g a 159: 14840248 t c 160: 14841901 g a 161: 14842227 a c 162:14842776 c t 163: 14843263 c g 164: 14886799 a g 165: 14887060 t c 166:14890588 g a 167: 14892192 c t 168: 14893868 a g 169: 14900711 t g 170:14901291 t a 171: 14903115 c a 172: 14916672 t c 173: 14920503 t a 174:14925694 t c 175: 14930044 g c 176: 14930395 a c 177: 14931113 a g 178:14932380 c g 179: 14937142 c t 180: 14938871 a g 181: 14940266 t c 182:14945976 c t 183: 14947005 t c 184: 14949091 a g 185: 14952249 a c 186:14955951 g a 187: 14957355 c t 188: 14957571 c t 189: 14958320 c t 190:14967763 a c 191: 14968075 t a 192: 14968622 t c 193: 14974256 a c 194:15000979 a g 195: 15002808 t g 196: 15002869 c t 197: 15003459 g a 198:15004691 c a 199: 15014070 t c 200: 15018850 g a 201: 15020436 g a 202:15020440 a g 203: 15056327 t c 204: 15064728 g a 205: 15073139 t c 206:15078999 t c 207: 15083283 a g 208: 15115316 c g 209: 15115423 c a 210:15120676 c t 211: 15123388 g a 212: 15130427 t a 213: 15137817 a c 214:15143098 c t 215: 15143140 c a 216: 15159625 a g 217: 15160203 c t 218:15167150 a g 219: 15174684 t a 220: 15183225 c t 221: 15183636 a t 222:15224071 t c 223: 15280085 t c 224: 15281410 c t 225: 15302421 a c 226:15328920 a c 227: 15328921 a t 228: 15329117 g a 229: 15336885 t a 230:15340434 t c 231: 15341050 c t 232: 15343408 g c 233: 15349577 g a 234:15358854 t c 235: 15359010 c t 236: 15360371 g a 237: 15360415 a c 238:15362712 a t 239: 15369500 c t 240: 15377503 t c 241: 15379111 a g 242:15381505 t c 243: 15395614 c g 244: 15418140 t c 245: 15427052 a g 246:15438583 g t 247: 15440219 a g 248: 15450658 a g 249: 15469944 t a 250:15497208 t a 251: 15529113 a g 252: 15531290 g t 253: 15536720 a g 254:15555005 a c 255: 15594759 c t 256: 15599617 c t 257: 15601332 a g 258:15603328 c g 259: 15605767 a g 260: 15642143 a g 261: 15644736 t a 262:15648823 c t 263: 15650129 c t 264: 15653803 g c 265: 15656922 c g 266:15663671 c a 267: 15675577 t a 268: 15675976 t c 269: 15676508 c t 270:15676597 c t 271: 15681214 t a 272: 15682739 t g 273: 15682925 c t 274:15684253 t g 275: 15687054 g a 276: 15688596 t c 277: 15689303 a g 278:15692480 g a 279: 15693924 c a 280: 15695029 g t 281: 15707183 t c 282:15714285 t c 283: 15714774 g a 284: 15716047 a c 285: 15718727 t c 286:15718927 g a 287: 15721987 a g 288: 15740761 c t 289: 15742761 c t 290:15743816 g a 291: 15751207 a g 292: 15751246 a t 293: 15751359 c t 294:15754104 t c 295: 15760186 c t 296: 15769673 a g 297: 15815282 c t 298:15817939 g a 299: 15833254 c a 300: 15835481 c g 301: 15851711 c t 302:15852041 c g 303: 15853469 g c 304: 15853824 a g 305: 15869264 t c 306:15869845 t a 307: 15870773 a g 308: 15872349 c g 309: 15896141 t c 310:15925924 t c 311: 16029732 t c 312: 16030763 c t 313: 16033046 g a 314:16044815 g t 315: 16059769 c t 316: 16060265 c g 317: 16063918 c t 318:16064730 g a 319: 16073916 g a 320: 16074294 t c 321: 16074744 a g 322:16093631 c t 323: 16100689 t g 324: 16107592 t g 325: 16124106 a g 326:16131138 t c 327: 16131244 c a 328: 16134155 a g 329: 16137958 c t 330:16139214 g a 331: 16140602 a g 332: 16140671 g t 333: 16140703 t g 334:16163942 g t 335: 16167455 g a 336: 16172690 t a 337: 16184901 c t 338:16185389 a g 339: 16187994 a g 340: 16293656 g c 341: 16305378 a g 342:16313571 a g 343: 16336578 g a 344: 16360879 c g 345: 16423969 a t 346:16423970 a t 347: 16423976 c g 348: 16431541 g c 349: 16448336 c g 350:16452007 a c 351: 16453773 a c 352: 16457724 c t 353: 16490654 t g 354:16495290 c t 355: 16540260 t c 356: 16544023 c a 357: 16556486 t a 358:16559936 c t 359: 16561463 a c 360: 16561464 a g 361: 16570267 c a 362:16583160 a g 363: 16595038 t a 364: 16649623 t a 365: 16663333 g a 366:16704084 c g 367: 16721418 a t 368: 16724279 c g 369: 16727706 c a 370:16728251 a g 371: 16743202 a t 372: 16745378 a g 373: 16751447 g a 374:16789636 g a 375: 16791935 a g 376: 16797023 a c 377: 16799064 c t 378:16799466 g a 379: 16804904 c t 380: 16807655 c t 381: 16808954 a g 382:16812750 a g 383: 16818812 t a 384: 16822411 a t 385: 16834673 a t 386:16836920 c g 387: 16842646 c t 388: 16846455 g c 389: 16846953 c t 390:16865096 c g 391: 16872214 a t 392: 16886895 t c 393: 16930714 t c 394:16943697 g a 395: 16962917 g a 396: 16979427 a g 397: 17004744 a t 398:17047704 g a 399: 17085341 c t 400: 17096273 t c 401: 17103628 g a 402:17108144 g a 403: 17119306 g a 404: 17129314 g a 405: 17129588 a c 406:17131642 g a 407: 17164499 a g 408: 17165382 t g 409: 17167672 a g 410:17174469 a t 411: 17178186 a g 412: 17180133 g a 413: 17182569 t c 414:17186173 t c 415: 17187712 g a 416: 17193070 c t 417: 17193084 g a 418:17194501 c t 419: 17209631 a t 420: 17219055 a c 421: 17220289 g a 422:17238397 a g 423: 17244984 t c 424: 17248128 g a 425: 17257839 c t 426:17262723 c g 427: 17278114 t c 428: 17281188 c t 429: 17290111 g a 430:17316238 t c 431: 17333820 t c 432: 17335050 t a 433: 17343694 g a 434:17367747 t c 435: 17369809 c t 436: 17370858 g a 437: 17373013 t c 438:17373879 a g 439: 17375880 g c 440: 17379865 t c 441: 17384067 t g 442:17393351 t a 443: 17394036 a g 444: 17396356 g a 445: 17397743 g a 446:17398741 a g 447: 17402470 c t 448: 17412963 a g 449: 17437115 a g 450:17473474 c t 451: 17475236 t c 452: 17480553 c t 453: 17486157 t c 454:17501700 t g 455: 17528110 t c 456: 17547768 g a 457: 17550231 a g 458:17553702 g c 459: 17570023 c t 460: 17571585 t a 461: 17580847 g c 462:17614190 c t 463: 17622058 t c 464: 17625750 c t 465: 17634579 a g 466:17639494 c g 467: 17644090 c t 468: 17647361 c t 469: 17650880 t g 470:17651536 a g 471: 17660174 g t 472: 17660498 c g 473: 17663768 g a 474:17667391 c t 475: 17668368 t c 476: 17668835 t c 477: 17693107 a g 478:17694468 a t 479: 17760514 g t 480: 17761607 g c 481: 17771810 g a 482:17773264 a g 483: 17794236 t c 484: 17794806 t a 485: 17801640 g a 486:17810038 c t 487: 17823360 a c 488: 17875449 t c 489: 17900831 c t 490:17902205 t a 491: 17903237 c t 492: 17910169 c t 493: 17970301 t c 494:18001282 t g 495: 18009431 a g 496: 18009678 a t 497: 18011006 t c 498:18011472 c t 499: 18012518 a g 500: 18016807 a g 501: 18017043 a c 502:18018684 t c 503: 18020417 t a 504: 18021881 a t 505: 18024253 c a 506:18025474 g a 507: 18030960 c t 508: 18031267 c t 509: 18067382 g a 510:18072464 c t 511: 18073416 a g 512: 18078999 c t 513: 18098017 g t 514:18101558 a g 515: 18102008 a c 516: 18158420 g a

[0026] It is to be understood that the above description is illustrativeand not restrictive. The scope of the invention should, therefore, bedetermined not with respect to the above description, but instead withrespect to the appended claims, along with the full scope of equivalentsto which the claims are entitled.

What is claimed is:
 1. A method of performing genetic analysiscomprising the steps of: a. scanning genomic DNA or derivativestherefrom from a plurality of individuals, wherein at least 10,000 basesare scanned, for genetic variants; b. identifying said genetic variantsin said genomic DNA or derivatives therefrom that occur in a pluralityof individuals; c. for at least said genomic variants that occur in aplurality of individuals, but not all of said at least 10,000 bases,scanning genomic DNA or derivatives therefrom from additionalindividuals to identify which of said genetic variants occur in saidadditional individuals; and d. based the results of step c), identifyingblocks of said variants.
 2. A method as recited in claim 1 furthercomprising the step of using said blocks of variants in an associationstudy, whereby said blocks of variants are associated with a phenotypictrait.
 3. The method as recited in claim 2 further comprising the stepof diagnosing said phenotypic trait using one or more variants that arein said block.
 4. The method as recited in claim 2 further comprisingthe step of using said variants associated with a phenotypic trait toidentify a potential drug target.
 5. The method as recited in claim 4further comprising the step of using said potential drug target in asmall molecule screening process.
 6. The method as recited in claim 1wherein said step of scanning genomic DNA or derivatives therefromcomprises the steps of: a. forming an array of probes a) complementaryto portions of a first sequence of said genomic DNA or derivativetherefrom and b) complementary to variants of said genomic DNA orderivative therefrom; b. hybridizing said genomic DNA or derivativetherefrom to said array; and c. identifying where said genomic DNA orderivative therefrom hybridize to said array.
 7. A method as recited inclaim 1 wherein said step of scanning genomic DNA comprises the step ofsequencing said genomic DNA with a gel based sequencer.
 8. The method asrecited in claim 1 wherein said step of scanning genomic DNA comprisesthe step of sequencing said genomic DNA with a capillary basedsequencer.
 9. The method as recited in claim 1 wherein only variantsthat occur in more than 10% of the said plurality of individuals areused in step c).
 10. The method as recited in claim 1 where said step ofscanning genomic DNA to identify which is said variants occur inadditional individuals comprises the steps of: a. exposing labeledgenomic DNA or a derivative thereof to a high density array of probescomplementary to said variants; and b. determining where said genomicDNA hybridizes to said high density array.
 11. The method as recited inclaim 1 where said step of scanning genetic DNA to identify which issaid variants occur in additional individuals comprises the use of anInvader assay.
 12. The method as recited in claim 1 where said step ofscanning genetic DNA to identify which is said variants occur inadditional individuals comprises the use of a Taqman assay.
 13. Themethod as recited in claim 1 wherein more than 1×10⁶ bases are scannedfor variants.
 14. The method as recited in claim 1 wherein more than1×10⁷ bases are scanned for variants.
 15. The method as recited in claim1 wherein more than 1×10⁸ bases are scanned for variants.
 16. The methodas recited in claim 1 wherein more than 1×10⁹ bases are scanned forvariants.
 17. The method as recited in claim 1 wherein introns arescanned for variants.
 18. The method as recited in claim 1 whereinintrons and exons are scanned for variants.
 19. The method as recited inclaim 1 wherein more than 10% of all the non-repeat genomic DNA from theorganism is scanned for variants.
 20. The method as recited in claim 1wherein more than 25% of all the non-repeat genomic DNA from an organismis scanned for variants.
 21. The method as recited in claim 1 whereinmore than 50% of all the non-repeat genomic DNA from an organism isscanned for variants.
 22. The method as recited in claim 1 wherein morethan 75% of all the non-repeat genomic DNA from an organism is scannedfor variants.
 23. The method as recited in claim 1 wherein said variantsare single nucleotide polymorphisms.
 24. The method as recited in claim2 further comprising the step of using the results of the associationstudy to stratify a patent population in a clinical trial.
 25. Themethod as recited in claim 2 further comprising the step of using theresults of the association study to stratify patents that respond to adrug from those who do not respond to a drug.
 26. The method as recitedin claim 2 further comprising the step of using the results of theassociation study to stratify patents that will show toxic response to adrug from patents that will not show toxic response to a drug.